simexin

simexin's Stars

• Illumina/hap.py

  Haplotype VCF comparison tools

  Language:C++423126

• Lasagne/Lasagne

  Lightweight library to build and train neural networks in Theano

  Language:Python3.9k945

• mozack/abra

  Assembly Based ReAligner

  Language:Java7212

• gt1/biobambam2

  Tools for early stage alignment file processing

  Language:C++9317

• ytdl-org/youtube-dl

  Command-line program to download videos from YouTube.com and other video sites

  Language:Python133k10.1k

• bcbio/bcbio-nextgen

  Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

  Language:Python994353

• atks/vt

  A tool set for short variant discovery in genetic sequence data.

  Language:C1943

• scikit-learn/scikit-learn

  scikit-learn: machine learning in Python

  Language:Python60.6k25.5k

• tensorflow/tensorflow

  An Open Source Machine Learning Framework for Everyone

  Language:C++187k74.4k

• mutalyzer/mutalyzer2

  HGVS variant nomenclature checker

  Language:Python9823

• counsyl/hgvs

  HGVS variant name parsing and generation

  Language:Python17180

• XX-net/XX-Net

  A proxy tool to bypass GFW.

  Language:Python33.1k7.7k

• vcftools/vcftools

  A set of tools written in Perl and C++ for working with VCF files, such as those generated by the 1000 Genomes Project.

  Language:C++510149

• arq5x/bedtools2

  bedtools - the swiss army knife for genome arithmetic

  Language:C946287

• genome/genome

  Core modules used by the GMS

  Language:Perl6457

• freebayes/freebayes

  Bayesian haplotype-based genetic polymorphism discovery and genotyping.

  Language:C++796264

• Bash-it/bash-it

  A community Bash framework.

  Language:Shell14.3k2.3k

• christoomey/vim-tmux-navigator

  Seamless navigation between tmux panes and vim splits

  Language:Vim Script5.5k336

• genome/gms

  The Genome Modeling System installer

  Language:Perl7822

• adamewing/bamsurgeon

  tools for adding mutations to existing .bam files, used for testing mutation callers

  Language:Python23786

• samtools/hts-specs

  Specifications of SAM/BAM and related high-throughput sequencing file formats

  Language:TeX662173

• broadgsa/gatk-protected

  Official code repository for GATK versions 1.0 through 3.7 (full licensed package). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository

  Language:Java143126

• samtools/bcftools

  This is the official development repository for BCFtools. See installation instructions and other documentation here http://samtools.github.io/bcftools/howtos/install.html

  Language:C687240

• samtools/htslib

  C library for high-throughput sequencing data formats

  Language:C816443

• samtools/samtools

  Tools (written in C using htslib) for manipulating next-generation sequencing data

  Language:C1.6k582

• broadinstitute/picard

  A set of command line tools (in Java) for manipulating high-throughput sequencing (HTS) data and formats such as SAM/BAM/CRAM and VCF.

  Language:Java990371

• broadgsa/gatk

  Official code repository for GATK versions 1.0 through 3.7 (core engine). For GATK 4 code, see the https://github.com/broadinstitute/gatk repository

  Language:Java296223

• broadinstitute/mutect

  MuTect -- Accurate and sensitive cancer mutation detection

  Language:Java9441

• broadinstitute/xtermcolor

  Python library for terminal color support (including 256-color support)

  Language:Python10510

• broadinstitute/gatk

  Official code repository for GATK versions 4 and up

  Language:Java1.7k596