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John M. Gaspar's repositories

Genrich

Detecting sites of genomic enrichment

Language:CMIT185 10 111

NGmerge

Merging paired-end reads and removing adapters

Language:CMIT44 1 25

DMRfinder

Identifying differentially methylated regions from MethylC-seq (bisulfite-sequencing) data

Language:PythonMIT26 6 18

MACS

MACS -- Model-based Analysis of ChIP-Seq

Language:PythonNOASSERTION6 1 1

ATAC-seq2

500

FlowClus

Filters and denoises pyrosequenced amplicons

Language:CNOASSERTION4 1 2

harvard

Language:Python300

ATAC-seq

Language:PythonMIT200

AmpliconTools

Language:PerlNOASSERTION1 10

Bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

Language:PerlGPL-3.01 10

rutgers

Language:Python100

bioconda-recipes

Conda recipes for the bioconda channel.

Language:Shell000

centrifuge

Classifier for metagenomic sequences

Language:C++GPL-3.0000

gemini

a lightweight db framework for disease and population genetics.

Language:PythonMIT000

gwu

Language:Perl010

metagen

Language:Python000

qiime

Quantitative Insights Into Microbial Ecology (QIIME): Official repository for software and unit tests

Language:Python010

simulator

PCR simulator

Language:C000

st_pipeline

ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

Language:PythonNOASSERTION000

stitch

Merging paired-end reads

Language:C000

tools-devteam

Contains a set of Galaxy Tools mostly written by the Galaxy Team.

Language:Python000

tools-iuc

Tool Shed repositories maintained and developed by the Intergalactic Utilities Commission

Language:PythonMIT010