Differential peak analysis with SnapATAC2 Version 1
Download RO-Crate
Run on GalaxyThis workflow takes a cell-type-annotated AnnData object (processed with SnapATAC2) and performs peak calling with MACS3 on the cell types. Next, a cell-by-peak matrix is constructed and differential accessibility tests are performed for comparison of either two cell types or one cell type with a background of all other cells. Lastly, differentially accessible marker regions for each cell type are identified.
Inputs
| ID | Name | Description | Type |
|---|---|---|---|
| 1 | Cell-type #1 | n/a |
|
| 2 | Cell-type #2 | n/a |
|
| Cell-type Annotated AnnData | Cell-type Annotated AnnData | n/a |
|
| chrom_sizes_new.txt | chrom_sizes_new.txt | n/a |
|
Steps
| ID | Name | Description |
|---|---|---|
| 4 | macs3 | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1 |
| 5 | cell-types_UMAP-plot | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_plotting/snapatac2_plotting/2.6.4+galaxy1 |
| 6 | merge_peaks | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1 |
| 7 | make_peak_matrix | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1 |
| 8 | Differential Expression between two cell types | Compares differentially accessible peaks between two cell types (f.ex. Memory B and Naive B cells) toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1 |
| 9 | Differential Expression compared to all cell types | Compares differentially accessible peaks between a cell type (f.ex. Naive B cell) and 30 random "background" cells of the other cell types toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1 |
| 10 | marker_regions | toolshed.g2.bx.psu.edu/repos/iuc/snapatac2_peaks_and_motif/snapatac2_peaks_and_motif/2.6.4+galaxy1 |
Outputs
| ID | Name | Description | Type |
|---|---|---|---|
| marker_regions | marker_regions | n/a |
|
| marker_regions-plot | marker_regions-plot | n/a |
|
Version History
Version 1 (earliest) Created 2nd Aug 2024 at 19:23 by Timon Schlegel
Initial commit
Open
mastere123665
Creators and SubmitterViews: 1001 Downloads: 120 Runs: 0
Created: 2nd Aug 2024 at 19:23
TagsThis item has not yet been tagged.
AttributionsNone
Related items
Teams: usegalaxy-eu
Organizations: Albert-Ludwigs-Universität Freiburg
https://orcid.org/0009-0001-3228-105X
A space managed by WorkflowHub administrators for teams that don't want/need to manage their own space.
Teams: IBISBA Workflows, NMR Workflow, UNLOCK, NanoGalaxy, Galaxy Climate, PNDB, IMBforge, COVID-19 PubSeq: Public SARS-CoV-2 Sequence Resource, LBI-RUD, Nick-test-team, usegalaxy-eu, Italy-Covid-data-Portal, UX trial team, Integrated and Urban Plant Pathology Laboratory, SARS-CoV-2 Data Hubs, lmjxteam2, virAnnot pipeline, Ay Lab, iPC: individualizedPaediatricCure, Harkany Lab, MOLGENIS, EJPRD WP13 case-studies workflows, Common Workflow Language (CWL) community, Testing, SeBiMER, IAA-CSIC, MAB - ATGC, Probabilistic graphical models, GenX, Snakemake-Workflows, ODA, IPK BIT, CO2MICS Lab, FAME, CHU Limoges - UF9481 Bioinformatique / CNR Herpesvirus, Quadram Institute Bioscience - Bioinformatics, HecatombDevelopment, Institute of Human Genetics, Testing RO Crates, Test Team, Applied Computational Biology at IEG/HMGU, INFRAFRONTIER workflows, OME, TransBioNet, OpenEBench, Bioinformatics and Biostatistics (BIO2 ) Core, VIB Bioinformatics Core, CRC Cohort, ICAN, MustafaVoh, Single Cell Unit, CO-Graph, emo-bon, TestEMBL-EBIOntology, CINECA, Toxicology community, Pitagora-Network, Workflows Australia, Medizinisches Proteom-Center, Medical Bioinformatics, AGRF BIO, EU-Openscreen, X-omics, ELIXIR Belgium, URGI, Size Inc, GA-VirReport Team, The Boucher Lab, Air Quality Prediction, pyiron, CAPSID, Edinburgh Genomics, Defragmentation TS, NBIS, Phytoplankton Analysis, Seq4AMR, Workflow registry test, Read2Map, SKM3, ParslRNA-Seq: an efficient and scalable RNAseq analysis workflow for studies of differentiated gene expression, de.NBI Cloud, Meta-NanoSim, ILVO Plant Health, EMERGEN-BIOINFO, KircherLab, Apis-wings, BCCM_ULC, Dessimoz Lab, TRON gGmbH, GEMS at MLZ, Computational Science at HZDR, Big data in biomedicine, TRE-FX, MISTIC, Guigó lab, Statistical genetics, Delineating Regions-of-interest for Mass Spectrometry Imaging by Multimodally Corroborated Spatial Segmentation, OLCF-WES, Bioinformatics Unit @ CRG, Bioinformatics Innovation Lab, BSC-CES, ELIXIR Proteomics, Black Ochre Data Labs, Zavolan Lab, Metabolomics-Reproducibility, Team Cardio, NGFF Tools, Bioinformatics workflows for life science, Workflows for geographic science, Pacific-deep-sea-sponges-microbiome, CSFG, SNAKE, Katdetectr, INFRAFRONTIER GmbH, PerMedCoE, Euro-BioImaging, EOSC-Life WP3 OC Team, cross RI project, ANSES-Ploufragan, SANBI Pathogen Bioinformatics, Biodata Analysis Group, DeSci Labs, Erasmus MC - Viroscience Bioinformatics, ARA-dev, Mendel Centre for Plant Genomics and Proteomics, Metagenomic tools, WorkflowEng, Polygenic Score Catalog, bpm, scNTImpute, Systems Biotechnology laboratory, Cimorgh IT solutions, MLme: Machine Learning Made Easy, Hurwitz Lab, Dioscuri TDA, Scipion CNB, System Biotechnology laboratory, yPublish - Bioinfo tools, NIH CFDE Playbook Workflow Partnership, MMV-Lab, EMBL-CBA, EBP-Nor, Evaluation of Swin Transformer and knowledge transfer for denoising of super-resolution structured illumination microscopy data, Bioinformatics Laboratory for Genomics and Biodiversity (LBGB), multi-analysis dFC, CholGen, RNA group, Plant Genomes Pipelines in Galaxy, Pathogen Genomic Laboratory, Chemical Data Lab, JiangLab, Pangenome database project, HP2NET - Framework for construction of phylogenetic networks on High Performance Computing (HPC) environment, Center for Open Bioimage Analysis, Generalized Open-Source Workflows for Atomistic Molecular Dynamics Simulations of Viral Helicases, Historical DNA genome skimming, QCDIS, Peter Menzel's Team, NHM Clark group, ESRF Workflow System (Ewoks), Kalbe Bioinformatics, Nextflow4Metabolomics, GBCS, CEMCOF, Jackson Laboratory NGS-Ops, Schwartz Lab, BRAIN - Biomedical Research on Adult Intracranial Neoplasms, Cancer Therapeutics and Drug Safety, Deepdefense, Mid-Ohio Regional Planning Commission, MGSSB, Institute for Human Genetics and Genomic Medicine Aachen, FengTaoSMU, EGA, Plant-Food-Research-Open, KrauthammerLab, Geo Workflows, grassland pDT, FunGIALab, CRIM - Computer Research Institute of Montréal, Medvedeva Lab, Metagenlab, FAIR-EASE, Protein-protein and protein-nucleic acid binding site prediction research, Culhane Lab, IDUN - Drug Delivery and Sensing, Edge Computing DAG Task Scheduling Research Group, Stratum corneum nanotexture feature detection using deep learning and spatial analysis: a non-invasive tool for skin barrier assessment, COPO, Taudière group, ErasmusMC Clinical Bioinformatics, interTwin, fluid flow modeling, EnrichDO, WorkflowResearch, Application Security - Test Crypt4GH solutions
Web page: Not specified
Space: Independent Teams
Public web page: https://usegalaxy.eu
