Jekyll 2025-10-23T19:56:37+00:00 https://training.galaxyproject.org/training-material/topics/epigenetics/feed.xml Epigenetics Recently added tutorials, slides, FAQs, and events in the epigenetics topic https://training.galaxyproject.org/training-material/assets/images/GTN-60px.png 📅 Workshop on high-throughput sequencing data analysis with Galaxy https://training.galaxyproject.org/training-material/events/2026-03-09-hts-workshop-freiburg.html 2025-10-23T19:56:37+00:00 This course introduces scientists to the data analysis platform Galaxy. The course is designed for beginners; no prior programming skills are required. Daniela Schneider https://training.galaxyproject.org/training-material/hall-of-fame/Sch-Da/ Diana Chiang Jurado https://training.galaxyproject.org/training-material/hall-of-fame/dianichj/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Amirhossein Naghsh Nilchi https://training.galaxyproject.org/training-material/hall-of-fame/Nilchia/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Paul Zierep https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ 🛠️ Hi-C Analysis with Galaxy Tutorial Workflow https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/hicexplorer/workflows/Hi-C_Analysis_with_Galaxy_Tutorial_Workflow.html 2025-08-11T07:08:27+00:00 Workflow for the GTN tutorial: "Hi-C analysis of Drosophila melanogaster cells using HiCExplorer". Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ 🛤️ Epigenetics data analysis with Galaxy https://training.galaxyproject.org/training-material/learning-pathways/epigenetics-from-zero.html 2025-03-14T15:10:05+00:00 Familiarize yourself with the Galaxy user interface and its most important features, then move on to analysis of genomic interval and deep-sequencing data with tools and tool suites like MACS2, bedtools and deepTools. 🛠️ Multisample Batch Correction with SnapATAC2 and Harmony https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-batch-correction-snapatac2/workflows/main_workflow.html 2025-02-28T07:41:57+00:00 This Workflow takes a dataset collection of single-cell ATAC-seq fragments and performs: - preprocessing - filtering - concatenation - dimension reduction - batch correction - leiden clustering Timon Schlegel https://training.galaxyproject.org/training-material/hall-of-fame/timonschlegel/ 📚 Multi-sample batch correction with Harmony and SnapATAC2 https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-batch-correction-snapatac2/tutorial.html 2025-02-28T07:41:57+00:00 Timon Schlegel https://training.galaxyproject.org/training-material/hall-of-fame/timonschlegel/ Diana Chiang Jurado https://training.galaxyproject.org/training-material/hall-of-fame/dianichj/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Timon Schlegel https://training.galaxyproject.org/training-material/hall-of-fame/timonschlegel/ 📅 Workshop on high-throughput sequencing data analysis with Galaxy https://training.galaxyproject.org/training-material/events/2025-03-10-hts-workshop-freiburg.html 2024-10-15T12:38:08+00:00 This course introduces scientists to the data analysis platform Galaxy. The course is a beginner course; no programming skills are required. Daniela Schneider https://training.galaxyproject.org/training-material/hall-of-fame/Sch-Da/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Amirhossein Naghsh Nilchi https://training.galaxyproject.org/training-material/hall-of-fame/Nilchia/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Engy Nasr https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ Paul Zierep https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ 📰 New Tutorial: Single-cell ATAC-seq standard processing with SnapATAC2 https://training.galaxyproject.org/training-material/news/2024/07/12/tutorial-snapatac-standard.html 2024-07-12T00:00:00+00:00 We are proud to announce that a new training, explaining the analysis of single cell ATAC-seq data with SnapATAC2 and Scanpy, is now available in the Galaxy Training Network. Timon Schlegel https://training.galaxyproject.org/training-material/hall-of-fame/timonschlegel/ 🛠️ Workflow - Standard processing of 10X single cell ATAC-seq data with SnapATAC2 https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/workflows/Standard-processing-of-10X-single-cell-ATAC-seq-data-with-SnapATAC2.html 2024-07-11T14:34:09+00:00 Workflow of Tutorial "Single-cell ATAC-seq standard processing with SnapATAC2". This workflow takes a fragment file as input and performs the standard steps of scATAC-seq analysis: filtering, dimension reduction, embedding and visualization of marker genes with SnapATAC2. In an alternative step, the fragment file can also be generated from a BAM file. Timon Schlegel https://training.galaxyproject.org/training-material/hall-of-fame/timonschlegel/ 📚 Single-cell ATAC-seq standard processing with SnapATAC2 https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-standard-processing-snapatac2/tutorial.html 2024-07-11T14:34:09+00:00 Single-cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) analysis is a method to decipher the chromatin states of the analyzed cells. In general, genes are only expressed in accessible (i.e. “open”) chromatin and not in closed chromatin. Timon Schlegel https://training.galaxyproject.org/training-material/hall-of-fame/timonschlegel/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Timon Schlegel https://training.galaxyproject.org/training-material/hall-of-fame/timonschlegel/ Wendi Bacon https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/ Martin Čech https://training.galaxyproject.org/training-material/hall-of-fame/martenson/ Armin Dadras https://training.galaxyproject.org/training-material/hall-of-fame/dadrasarmin/ 📅 Workshop on high-throughput sequencing data analysis with Galaxy https://training.galaxyproject.org/training-material/events/2024-07-22-freiburg-july.html 2024-07-10T17:01:39+00:00 This course introduces scientists to the data analysis platform Galaxy. The course is a beginner course; no programming skills are required. Anika Erxleben https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Amirhossein Naghsh Nilchi https://training.galaxyproject.org/training-material/hall-of-fame/Nilchia/ Teresa Müller https://training.galaxyproject.org/training-material/hall-of-fame/teresa-m/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Engy Nasr https://training.galaxyproject.org/training-material/hall-of-fame/EngyNasr/ Paul Zierep https://training.galaxyproject.org/training-material/hall-of-fame/paulzierep/ 🛠️ CUT&RUN https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/cut_and_run/workflows/main_workflow.html 2024-03-06T07:59:37+00:00 CUT&RUN workflow used in GTN Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ 📚 CUT&RUN data analysis https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/cut_and_run/tutorial.html 2024-03-06T07:59:37+00:00 In many organism, transcription factors (TF) play an important tole in the regulation of the gene expression. In human, we have up to 2,800 proteins and more than 1,600 are Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Lucille Delisle https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ 🛠️ Infinium Human Methylation BeadChip https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/ewas-suite/workflows/Infinium-Human-Methylation-BeadChip.html 2023-10-23T10:11:26+00:00 The workflow containes the step to perpare the data for and run Galaxy Infinium Human Methylation BeadChip tool that represents many popular algorithms for detecting somatic genetic alterations from genome and exome data Katarzyna Kamieniecka https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/ Khaled Jum'ah https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/ Krzysztof Poterlowicz https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/ 📚 Pre-processing of 10X Single-Cell ATAC-seq Datasets https://training.galaxyproject.org/training-material/topics/single-cell/tutorials/scatac-preprocessing-tenx/tutorial.html 2023-04-24T18:23:20+00:00 Similar to bulk ATAC-Seq, single-cell ATAC-Seq (scATAC-seq) leverages the hyperactive Tn5 Transposase to profile open chromatin regions but at single-cell resolution. Thus helps in understanding cell type-specific chromatin accessibility from a heterogeneous cell population. Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Mehmet Tekman https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/ Wendi Bacon https://training.galaxyproject.org/training-material/hall-of-fame/nomadscientist/ Timon Schlegel https://training.galaxyproject.org/training-material/hall-of-fame/timonschlegel/ Marisa Loach https://training.galaxyproject.org/training-material/hall-of-fame/MarisaJL/ ❓ UCSC import: what should my file look like? https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/faqs/ucsc_import.html 2022-03-02T15:46:20+00:00 ~2020 lines, with the following header line: Lucille Delisle https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ Hans-Rudolf Hotz https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/ Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ ❓ Is it possible to subsample some samples if you have more reads? https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/faqs/subsampling.html 2022-03-02T15:46:20+00:00 Lucille Delisle https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ ❓ Changing the heatmap colours https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/faqs/heatmap_colours.html 2022-03-02T15:46:20+00:00 You can change the heatmap color, by expanding the Show advanced options section. There are many options here, including setting the colors. Lucille Delisle https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ Hans-Rudolf Hotz https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/ Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ ❓ In bowtie 2 parameters, in place of 1000 for other experiments, should we mention the median fragment length observed in our library? https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/faqs/bowtie_parameters.html 2022-03-02T15:46:20+00:00 Not the median fragment length but the maximum fragment length you expect. However, you will see that in illumina sequencers, the longer the fragments are the less efficiently they are sequenced so long fragment length pairs are not very numerous. Lucille Delisle https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ Hans-Rudolf Hotz https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/ Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ ❓ Automatically trim adapters (without providing custom sequences) https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/faqs/adapter_trimming.html 2022-03-02T15:46:20+00:00 There are many tools for this: Trimmomatic, Trim Galore, and a few others (search: “Trim”). Lucille Delisle https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ Hans-Rudolf Hotz https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/ Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ 🖼️ Introduction to ATAC-Seq data analysis https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/slides.html 2021-04-08T13:47:23+00:00 Where does my data come from? Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ Lucille Delisle https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ 🎥 Recording of Introduction to ATAC-Seq data analysis https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/recordings/#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00 A 15M long recording is now available. Lucille Delisle https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ 🎥 Recording of ATAC-Seq data analysis https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/recordings/#tutorial-recording-15-february-2021 2021-02-15T00:00:00+00:00 A 1H50M long recording is now available. Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ 🛠️ Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/tal1-binding-site-identification/workflows/tal1-binding-site-identification-workflow.html 2020-10-07T11:07:32+00:00 Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) 🛠️ ATAC-seq GTM https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/workflows/main_workflow.html 2019-09-02T16:17:33+00:00 atac-seq Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ 📚 ATAC-Seq data analysis https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/atac-seq/tutorial.html 2019-09-02T16:17:33+00:00 In many eukaryotic organisms, such as humans, the genome is tightly packed and organized with the help of nucleosomes (chromatin). A nucleosome is a complex formed by eight histone proteins that is wrapped with ~147bp of DNA. When the DNA is being actively transcribed into RNA, the DNA will be opened and loosened from the nucleosome complex. Many factors, such as the chromatin structure, the position of the nucleosomes, and histone modifications, play an important role in the organization and accessibility of the DNA. Consequently, these factors are also important for the activation and inactivation of genes. Assay for Transposase-Accessible Chromatin using sequencing (ATAC-Seq) is a method to investigate the accessibility of chromatin and thus a method to determine regulatory mechanisms of gene expression. The method can help identify promoter regions and potential enhancers and silencers. A promoter is the DNA region close to the transcription start site (TSS). It contains binding sites for transcription factors that will recruit the RNA polymerase. An enhancer is a DNA region that can be located up to 1 Mb downstream or upstream of the promoter. When transcription factors bind an enhancer and contact a promoter region, the transcription of the gene is increased. In contrast, a silencer decreases or inhibits the gene’s expression. ATAC-Seq has become popular for identifying accessible regions of the genome as it’s easier, faster and requires less cells than alternative techniques, such as FAIRE-Seq and DNase-Seq. Lucille Delisle https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ Maria Doyle https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/ Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Lucille Delisle https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ Gildas Le Corguillé https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/ Hans-Rudolf Hotz https://training.galaxyproject.org/training-material/hall-of-fame/hrhotz/ 🛠️ GTN - ChIP Seq - Formation Of Super Structures On Xi https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/workflows/formation_of_super_structures_on_xi.html 2018-09-17T07:13:05+00:00 Friederike Dündar Anika Erxleben https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Vivek Bhardwaj Fidel Ramirez Leily Rabbani Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ 🖼️ ChIP-seq data analysis https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/slides.html 2018-09-17T07:13:05+00:00 ChIP-seq Leily Rabbani https://training.galaxyproject.org/training-material/hall-of-fame/LeilyR/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ Joachim Wolff https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/ Leily Rabbani https://training.galaxyproject.org/training-material/hall-of-fame/LeilyR/ 📚 Formation of the Super-Structures on the Inactive X https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/formation_of_super-structures_on_xi/tutorial.html 2018-09-17T07:13:05+00:00 Within a cell nucleus, the DNA is tightly-packed and the chromatin is spatially distributed with different levels and scales of organizations. Friederike Dündar https://training.galaxyproject.org/training-material/hall-of-fame/friedue/ Anika Erxleben https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Vivek Bhardwaj https://training.galaxyproject.org/training-material/hall-of-fame/vivekbhr/ Fidel Ramirez https://training.galaxyproject.org/training-material/hall-of-fame/fidelram/ Leily Rabbani https://training.galaxyproject.org/training-material/hall-of-fame/LeilyR/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Anup Kumar https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Gildas Le Corguillé https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/ Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ Joachim Wolff https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/ Leily Rabbani https://training.galaxyproject.org/training-material/hall-of-fame/LeilyR/ Martin Čech https://training.galaxyproject.org/training-material/hall-of-fame/martenson/ Armin Dadras https://training.galaxyproject.org/training-material/hall-of-fame/dadrasarmin/ 🖼️ EWAS Epigenome-Wide Association Studies Introduction https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/ewas-suite/slides.html 2018-08-27T08:04:21+00:00 What is the topic? Katarzyna Kamieniecka https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/ Krzysztof Poterlowicz https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Katarzyna Kamieniecka https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ kpbioteam https://training.galaxyproject.org/training-material/hall-of-fame/kpbioteam/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ 📚 Infinium Human Methylation BeadChip https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/ewas-suite/tutorial.html 2018-08-27T08:04:21+00:00 This tutorial is based on Hugo W, Shi H, Sun L, Piva M et al.: Non-genomic and Immune Evolution of Melanoma Acquiring MAPKi Resistance Hugo et al. 2015. Katarzyna Kamieniecka https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/ Khaled Jum'ah https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/ Krzysztof Poterlowicz https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Katarzyna Kamieniecka https://training.galaxyproject.org/training-material/hall-of-fame/kkamieniecka/ Khaled Jum'ah https://training.galaxyproject.org/training-material/hall-of-fame/khaled196/ Krzysztof Poterlowicz https://training.galaxyproject.org/training-material/hall-of-fame/poterlowicz-lab/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ kpbioteam https://training.galaxyproject.org/training-material/hall-of-fame/kpbioteam/ Mélanie Petera https://training.galaxyproject.org/training-material/hall-of-fame/melpetera/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ 📚 Hi-C analysis of Drosophila melanogaster cells using HiCExplorer https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/hicexplorer/tutorial.html 2018-02-23T11:09:57+00:00 In this HiCExplorer tutorial we will generate and plot a Hi-C contact matrix. Joachim Wolff https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/ Fidel Ramirez https://training.galaxyproject.org/training-material/hall-of-fame/fidelram/ Vivek Bhardwaj https://training.galaxyproject.org/training-material/hall-of-fame/vivekbhr/ Ekaterina Polkh https://training.galaxyproject.org/training-material/hall-of-fame/polkhe/ Tristan Reynolds https://training.galaxyproject.org/training-material/hall-of-fame/tflowers15/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Joachim Wolff https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Mehmet Tekman https://training.galaxyproject.org/training-material/hall-of-fame/mtekman/ Anup Kumar https://training.galaxyproject.org/training-material/hall-of-fame/anuprulez/ Torsten Houwaart https://training.galaxyproject.org/training-material/hall-of-fame/torhou/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ 🛠️ Identification Of The Binding Sites Of The Estrogen Receptor - Qc Mapping https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/workflows/qc_mapping.html 2017-09-18T20:09:29+00:00 Identification of the binding sites of the Estrogen receptor 🛠️ Identification Of The Binding Sites Of The Estrogen Receptor - Chip Seq https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/estrogen-receptor-binding-site-identification/workflows/chip_seq.html 2017-09-18T20:09:29+00:00 Identification of the binding sites of the Estrogen receptor 🛠️ Workflow Methylation Seq https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/methylation-seq/workflows/methylation-seq.html 2017-09-13T09:19:44+00:00 DNA Methylation data analysis 🖼️ Introduction to ChIP-Seq data analysis https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/introduction-chip-seq/slides.html 2017-06-12T08:10:40+00:00 What is ChIP sequencing? Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ 📚 DNA Methylation data analysis https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/methylation-seq/tutorial.html 2017-02-16T08:40:49+00:00 We will use a small subset of the original data. If we would do the computation on the orginal data the computation time for a tutorial is too long. To show you all necessary steps for Methyl-Seq we decided to use a subset of the data set. In a second step we use precomputed data from the study to show you different levels of methylation. We will consider samples from normal breast cells (NB), fibroadenoma (noncancerous breast tumor, BT089), two invasive ductal carcinomas (BT126, BT198) and a breast adenocarcinoma cell line (MCF7). Joachim Wolff https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/ Devon Ryan https://training.galaxyproject.org/training-material/hall-of-fame/dpryan79/ Verena Moosmann https://training.galaxyproject.org/training-material/hall-of-fame/VerenaMoo/ Pavankumar Videm https://training.galaxyproject.org/training-material/hall-of-fame/pavanvidem/ Wolfgang Maier https://training.galaxyproject.org/training-material/hall-of-fame/wm75/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Gildas Le Corguillé https://training.galaxyproject.org/training-material/hall-of-fame/lecorguille/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ 📚 Identification of the binding sites of the T-cell acute lymphocytic leukemia protein 1 (TAL1) https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/tal1-binding-site-identification/tutorial.html 2016-12-20T14:12:55+00:00 This tutorial uses ChIP-seq datasets from a study published by Wu et al. 2014. The goal of this study was to investigate “the dynamics of occupancy and the role in gene regulation of the transcription factor TAL1, a critical regulator of hematopoiesis, at multiple stages of hematopoietic differentiation.” Mallory Freeberg https://training.galaxyproject.org/training-material/hall-of-fame/malloryfreeberg/ Mo Heydarian https://training.galaxyproject.org/training-material/hall-of-fame/moheydarian/ Vivek Bhardwaj https://training.galaxyproject.org/training-material/hall-of-fame/vivekbhr/ Joachim Wolff https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/ Anika Erxleben https://training.galaxyproject.org/training-material/hall-of-fame/erxleben/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Mallory Freeberg https://training.galaxyproject.org/training-material/hall-of-fame/malloryfreeberg/ Friederike Dündar https://training.galaxyproject.org/training-material/hall-of-fame/friedue/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ Fidel Ramirez https://training.galaxyproject.org/training-material/hall-of-fame/fidelram/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/ Niall Beard https://training.galaxyproject.org/training-material/hall-of-fame/njall/ Maria Doyle https://training.galaxyproject.org/training-material/hall-of-fame/mblue9/ Martin Čech https://training.galaxyproject.org/training-material/hall-of-fame/martenson/ Armin Dadras https://training.galaxyproject.org/training-material/hall-of-fame/dadrasarmin/ 🖼️ Introduction to DNA Methylation data analysis https://training.galaxyproject.org/training-material/topics/epigenetics/tutorials/introduction-dna-methylation/slides.html 2016-10-05T15:07:38+00:00 DNA Methylation data analysis Joachim Wolff https://training.galaxyproject.org/training-material/hall-of-fame/joachimwolff/ Yvan Le Bras https://training.galaxyproject.org/training-material/hall-of-fame/yvanlebras/ Bérénice Batut https://training.galaxyproject.org/training-material/hall-of-fame/bebatut/ Saskia Hiltemann https://training.galaxyproject.org/training-material/hall-of-fame/shiltemann/ Helena Rasche https://training.galaxyproject.org/training-material/hall-of-fame/hexylena/ Florian Heyl https://training.galaxyproject.org/training-material/hall-of-fame/heylf/ Lucille Delisle https://training.galaxyproject.org/training-material/hall-of-fame/lldelisle/ Cristóbal Gallardo https://training.galaxyproject.org/training-material/hall-of-fame/gallardoalba/ Nicola Soranzo https://training.galaxyproject.org/training-material/hall-of-fame/nsoranzo/ William Durand https://training.galaxyproject.org/training-material/hall-of-fame/willdurand/ Björn Grüning https://training.galaxyproject.org/training-material/hall-of-fame/bgruening/