Pinned Repositories
abf2heatmap
simple parser tool for ePhys .abf data
annotator
batch_correction_scripts
cwl wrapper for seurat batch effect correction package
bfx
bioinformatics scripts
clip_analysis
CLIPSEQ analysis tools
clustering_tools
single cell clustering tools written for cwl workflows
convertTSV
converts TSV files to sparse/dense mtx files and H5 files, or the other way around.
docker
dockerfiles for various envs
junction-counter
counts reads that support excluded exon-intron junctions
singularity
Singularity files, mostly just pulling from docker
byee4's Repositories
byee4/junction-counter
counts reads that support excluded exon-intron junctions
byee4/convertTSV
converts TSV files to sparse/dense mtx files and H5 files, or the other way around.
byee4/batch_correction_scripts
cwl wrapper for seurat batch effect correction package
byee4/bedtools_closest_issue
byee4/clip_analysis_legacy
byee4/clustering
byee4/common-workflow-language
Repository for CWL Specifications. Use https://www.biostars.org/t/cwl/ for support.
byee4/decomposition
byee4/deepTools
Tools to process and analyze deep sequencing data.
byee4/DESeq2
DESeq2 CWL tool for automated differential expression analysis
byee4/eclipdemux
demultiplexing script for paired-end eCLIP reads
byee4/featureCounts
featureCounts cwl wrapper
byee4/GGR-cwl
CWL tools and workflows for GGR
byee4/gscripts
General Use Scripts and Helper functions
byee4/module_creation_scripts
scripts for creating modules on TSCC
byee4/rbp-maps
splicing and feature maps for RBPs
byee4/rnaseq_analysis
functions and scripts for analyzing RNASEQ (mostly bulk) data
byee4/sailor
CWL+Singularity implementation of an RNA editing workflow
byee4/ShapeSeq_Shiskin
This repo contains analysis script specific to data generated using the in-house Shiskin protocol for ShapeSeq
byee4/singlecell_rnaseq_pipeline
single cell RNA seq processing pipeline
byee4/singularity-tools
collection of command line tools for working with Singularity and Docker
byee4/toil
A scalable, efficient, cross-platform and easy-to-use workflow engine in pure Python
byee4/trackhub
create, manage, and upload track hubs for use in the UCSC genome browser
byee4/workflows
Community maintained workflows & tools (with examples)