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apollo3-testci

Fork for experimenting with github workflows

asciigenome

Text Only Genome Viewer!

bioconda-recipes

Conda recipes for the bioconda channel.

bioconda-utils

Utilities for building and managing bioconda recipes

bioinformatics-cafe

Unsorted scripts for bioinformatics

bwa-meth

align BS-Seq reads and extract methylation without intermediate temp files

cancer-variants-pipeline

Pipeline for somatic variant detection from NGS data

cnv_facets

Somatic copy variant caller (CNV) for next generation sequencing

colors

List of 256 color codes for Xterm including an example of the color, Xterm Name, Xterm Number and HEX code.

companion

A genome annotation tool for more than just protists

deeptools

Tools to process and analyze deep sequencing data.

dnascent

Software for detecting regions of BrdU and EdU incorporation in Oxford Nanopore reads.

epic2

Ultraperformant reimplementation of SICER

exceltocsv

Command-line exporter of MS Excel files to CSV format

fix-onedrive-zip

Fix OneDrive Zip files >4Gig

fxstat

Fast and easy stats for FASTA and FASTQ files

genomegraphs

Command line program to visualize genomic data

github-markdown-toc

Easy TOC creation for GitHub README.md

htsjdk

A Java API for high-throughput sequencing data (HTS) formats.

htsjdk-1.141

Fork of htsjdk version 1.141. Mostly for the purpose of adapting it to other projects.

htsjdk-test

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

illumina-450k-oxbs

Code accompanying the manuscript "Accurate measurement of 5-methylcytosine and 5-hydroxymethylcytosine in human cerebellum DNA by oxidative bisulfite on an array (OxBS-array)"

java-cafe

A variety of bioinformatics programs written in Java

jawk

Java AWK interpreter/compiler

quadratic-programming-deconvolution

A tutorial on quadratic programming for deconvolution of mixed cell populations using R

rebuilt-enhanced-methyl-seq

Code supporting the article "Enhanced Methylation Analysis by Recovery of Unsequenceable Fragments", McInroy et al., 2016

reference-code

Code used in published material like articles or theses.

rnaseq-downsample-effect

Effect of downsampling the number of reads on differential gene expression from RNAseq experiments

sequencematcher

Match query sequences against reference sequences