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Bioconductor2 months ago
Branch-specific workflows | devel branch | RELEASE_3_17 branch | RELEASE_* branches | Session Info
rworkflows 1.0.12Authors: `r auths <- eval(parse(text = gsub('person','c',utils::packageDescription('rworkflows', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`bioconductor.Rmd
Dependency graph2 months ago
Create | Install required packages | Create graph | Save data | Count stars/clones/views | Show | rworkflow depgraph | Identify highly downloaded packages | Assess R repository usage | Session Info
rworkflows 1.0.12Authors: `r auths <- eval(parse(text = gsub('person','c',utils::packageDescription('rworkflows', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`depgraph.Rmd
Docker/Singularity Containers2 months ago
Installation | Method 1: via Docker | NOTES | Method 2: via Singularity | Usage | Session Info
rworkflows 1.0.12Authors: `r auths <- eval(parse(text = gsub("person","c",utils::packageDescription("rworkflows", fields = "Authors@R"))));paste(auths[names(auths)=="given"],auths[names(auths)=="family"], collapse = ", ")`docker.Rmd
Repositories report2 months ago
Install required packages | Get all packages per repo | Upset plot | Save results | Session Info
rworkflows 1.0.12Authors: `r auths <- eval(parse(text = gsub('person','c',utils::packageDescription('rworkflows', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`repos.Rmd
Get Started2 months ago
GitHub Secrets | use_workflow | dynamic action | static workflow | use_badges | use_dockerfile | Templates | README | Vignette: Get started | Vignette: docker | Adding Python | Using Python | Using conda | Session Info
rworkflows 1.0.12Authors: `r auths <- eval(parse(text = gsub('person','c',utils::packageDescription('rworkflows', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`rworkflows.Rmd
Get started8 months ago
Overview | Introduction | Data | Installation | Running MotifPeeker | Load the package | Load the example datasets | Prepare input data | Peak Files | Alignment Files | Genome Build | Motif Files | Run MotifPeeker | Required Inputs | Optional Inputs | Other Options | Runtime Guidance | Outputs | Troubleshooting | Future Enhancements | Session Info
MotifPeeker 1.5.0Hiranyamaya Dash MotifPeeker.Rmd
EpiCompare: Getting started1 years ago
Overview | Introduction | Data | Installation | Running EpiCompare | Load package and example datasets | Prepare input data | Peaklist | Blacklist | Picard summary files | Reference file | Output Directory | Run EpiCompare | Optional plots | Other options | Output | Future Enhancements | Code used to generate the example report | Session Information
EpiCompare 1.17.0Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`EpiCompare.Rmd
Troubleshooting2 years ago
MEME Suite Related | MotifPeeker() Related | Session Info
MotifPeeker 1.5.0Hiranyamaya Dash troubleshooting.Rmd
Example report3 years ago
EpiArchives is a public archive for interactive HTML reports generated by EpiCompare and the associated code used to create them. | Home | Reports | atac_dnase_chip_example | atac_dnase_example | Session Information
EpiCompare 1.17.0Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`example_report.Rmd
Getting started3 years ago
Introduction | Setup | Run cell-type enrichment tests | 1. Prepare input data | CellTypeDataset | CTD levels | Plot CTD mean_exp | Gene list | 2. Run cell type enrichment tests | Hyperparameters | Parallelisation | Docker | Installation | Method 1: via Docker | Method 2: via Singularity | Usage | Session Info | References
EWCE 1.21.0Authors: Alan Murphy, Brian Schilder, and Nathan SkeneEWCE.Rmd
Extended examples3 years ago
Setup | Run cell-type enrichment tests | Introduction | Prepare input data | CellTypeDataset | CTD levels | Gene lists | Gene formats and species | Notes on orthogene | Setting analysis parameters | Enrichment tests | Default tests | Parallelisation | Plot results | Control for transcript length and GC-content | Test different CTD levels | Plot results from multiple sets of enrichment results | Create a CellTypeDataset | Loading datasets | Convert single-cell formats | Correct gene symbols | Drop genes | Normalization [Optional] | SingleCellExperiment | Calculate specificity matrices | Generate CellTypeDataset | Merge two single-cell datasets | Load hypothalamus dataset | Fix bad MGI symbols | Merge CTD | Drop uninformative genes | Understanding specificity matrices | Run conditional cell-type enrichment tests | Prepare data | Controlling for expression in another cell type | Merge and plot results | Gene set enrichment analysis controlling for cell type expression | Controlling for multiple cell types | Apply to transcriptomic data | Analysing single transcriptome study | Generating bootstrap plots for transcriptomes | Merging multiple transcriptome studies | Load data | Run EWCE analysis | Session Info | References
EWCE 1.21.0Authors: Alan Murphy, Brian Schilder, and Nathan Skeneextended.Rmd
Docker/Singularity Containers4 years ago
DockerHub | Installation | Method 1: via Docker | NOTES | Method 2: via Singularity | Usage | Session Info
EpiCompare 1.17.0Authors: `r auths <- eval(parse(text = gsub('person','c',read.dcf('../DESCRIPTION', fields = 'Authors@R'))));paste(auths[names(auths)=='given'],auths[names(auths)=='family'], collapse = ', ')`docker.Rmd