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chowda

Python module for analysis of CLAMS (comprehensive lab animal monitoring system) data

chromosomemappings

This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

citar

Emacs package to quickly find and act on bibliographic references, and edit org, markdown, and latex academic documents.

cnvkit

Copy number variant detection from targeted DNA sequencing

common-workflow-language

Repository for CWL Specifications. Use https://www.biostars.org/t/cwl/ for support.

compcoder

compute-gpu-installation

conda-smithy

The tool for managing conda-forge feedstocks.

crossmap

CrossMap is a python program to lift over genome coordinates from one genome version to another.

curl-feedstock

A conda-smithy repository for curl.

datasets

My datasets - Original data or Aggregated / cleaned / restructured existing datasets. Released here under Creative Commons B

deepvariant

DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

degreport

Create a cromphensive report of DEG list coming from any analysis of RNAseq data

delicious

Source code to Delicious bookmarking site, pull requests welcome

dge-vis

disambiguate

Disambiguation algorithm for reads aligned to human and mouse genomes using Tophat or BWA mem

duphold

don't get DUP'ed or DEL'ed by your putative SVs.

dvc.org

🔗 DVC website and documentation

exomecov

utils functions for exome coverage plots as quality controls

flotilla

Reproducible machine learning analysis of gene expression and alternative splicing data

flycheck

Modern on the fly syntax checking for GNU Emacs

fusion-gene-blacklist

blacklist of fusion genes

g-quad

Calculates the G-quadraplex score for a FASTA file of sequences

geneimpacts

prioritize effects of variant annotations from VEP, SnpEff, et al.

gffcompare

classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

gffutils

GFF and GTF file manipulation and interconversion

gffutils-utils

Collection of one off type scripts using a gffutils database

hera

hisat2

Graph-based alignment (Hierarchical Graph FM index)

homebrew

:beer: The missing package manager for OS X.