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4tu_mpeseq

4-tu_MPEseq data processing and splicing kinetics

cat_rename_init

Sub module for renaming and concatenating .fastq files and initiating workflows on BigPurple.

chipseq

Paired-end ChIPseq data processing workflow designed for execution on the BigPurple HPC. Primary software used: FastQC, Fastp, Bowtie 2, MACS2, MultiQC

chrome_chipseq

CHROME ChIPseq analysis associated with GEO: GSE190413

cut-run

Paired-end CUT and RUN data processing workflow designed for execution on the BigPurple HPC. Primary software used: FastQC, Fastp, Bowtie 2, SEACR, MultiQC

cvrcfunc

cvrcseq

A collection of snakemake workflows for RNAseq, CUT-RUN, and ChIPseq analysis

quant_seq_analysis

rna_seq_timecourse

rnaseq_pe

Paired-end RNAseq data processing workflow designed for execution on the BigPurple HPC. Primary software used: FastQC, Fastp, STAR, featureCounts, MultiQC

rnaseq_pe_hisat2_stringtie

Paired-end RNAseq data processing workflow designed for execution on the BigPurple HPC. Primary software used: FastQC, Fastp, HISAT2, StringTie, MultiQC

rnaseq_pe_hisat2_stringtie_novel_transcripts

Paired-end RNAseq data processing workflow designed for execution on the BigPurple HPC. This version enables assembly of novel transcript isoforms. Primary software used: FastQC, Fastp, HISAT2, StringTie, MultiQC

rnaseq_se

rnavelo

RNA velocity workflow. Needs a lot of work.

scanpy_functions

scripts to run scanpy some functions

tecan_analysis