Pinned Repositories
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
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
mgildea87's Repositories
mgildea87/CVRCFunc
mgildea87/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
mgildea87/ChIPseq
Paired-end ChIPseq data processing workflow designed for execution on the BigPurple HPC. Primary software used: FastQC, Fastp, Bowtie 2, MACS2, MultiQC
mgildea87/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
mgildea87/RNAseq_PE
Paired-end RNAseq data processing workflow designed for execution on the BigPurple HPC. Primary software used: FastQC, Fastp, STAR, featureCounts, MultiQC
mgildea87/CHROME_ChIPseq
CHROME ChIPseq analysis associated with GEO: GSE190413
mgildea87/CVRCseq
A collection of snakemake workflows for RNAseq, CUT-RUN, and ChIPseq analysis
mgildea87/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
mgildea87/4tu_MPEseq
4-tu_MPEseq data processing and splicing kinetics
mgildea87/cat_rename_init
Sub module for renaming and concatenating .fastq files and initiating workflows on BigPurple.
mgildea87/Quant_seq_analysis
mgildea87/RNA_seq_timecourse
mgildea87/RNAseq_SE
mgildea87/RNAvelo
RNA velocity workflow. Needs a lot of work.
mgildea87/scanpy_functions
scripts to run scanpy some functions
mgildea87/TECAN_analysis