bkohrn

bkohrn's Stars

• exaloop/codon

  A high-performance, zero-overhead, extensible Python compiler with built-in NumPy support

  Language:Python15.4k140435526

• google/deepvariant

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

  Language:Python3.3k153872738

• nextflow-io/nextflow

  A DSL for data-driven computational pipelines

  Language:Groovy2.9k893.4k666

• broadinstitute/gatk

  Official code repository for GATK versions 4 and up

  Language:Java1.8k1554.6k602

• samtools/samtools

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

  Language:C1.7k981.3k581

• lh3/bwa

  Burrow-Wheeler Aligner for short-read alignment (see minimap2 for long-read alignment)

  Language:C1.6k107310554

• 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:Java996157812372

• pysam-developers/pysam

  Pysam is a Python package for reading, manipulating, and writing genomics data such as SAM/BAM/CRAM and VCF/BCF files. It's a lightweight wrapper of the HTSlib API, the same one that powers samtools, bcftools, and tabix.

  Language:Cython81047937277

• bwa-mem2/bwa-mem2

  The next version of bwa-mem

  Language:C++73836216102

• Ensembl/ensembl-vep

  The Ensembl Variant Effect Predictor predicts the functional effects of genomic variants

  Language:Perl470281.1k157

• mskcc/vcf2maf

  Convert a VCF into a MAF, where each variant is annotated to only one of all possible gene isoforms

  Language:Perl38079322219

• fulcrumgenomics/fgbio

  Tools for working with genomic and high throughput sequencing data.

  Language:Scala3221941970

• AlexandrovLab/SigProfilerExtractor

  SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

  Language:Python1562121554

• AstraZeneca-NGS/VarDictJava

  VarDict Java port

  Language:Java1324028955

• AlexandrovLab/SigProfilerMatrixGenerator

  SigProfilerMatrixGenerator creates mutational matrices for all types of somatic mutations. It allows downsizing the generated mutations only to parts for the genome (e.g., exome or a custom BED file). The tool seamlessly integrates with other SigProfiler tools.

  Language:Python1032314338

• AlexandrovLab/SigProfilerPlotting

  SigProfilerPlotting provides a standard tool for displaying all types of mutational signatures as well as all types of mutational patterns in cancer genomes. The tool seamlessly integrates with other SigProfiler tools.

  Language:Python47141514

• AlexandrovLab/SigProfilerSingleSample

  SigProfilerSingleSample allows attributing a known set of mutational signatures to an individual sample. The tool identifies the activity of each signature in the sample and assigns the probability for each signature to cause a specific mutation type in the sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting.

  Language:Python2314232

• Kennedy-Lab-UW/Duplex-Seq-Pipeline

  A standalone end-to-end data analysis pipeline for Duplex Sequencing

  Language:HTML215439

• FredHutch/workflow-template-nextflow

  Template for building a small workflow in Nextflow

  Language:HTML168013

• jmkidd/dogmap

  pipeline for dog WGS alignment

  Language:Python13315

• PF2-pasteur-fr/checkMyIndex

  Search for a set of compatible indexes for your sequencing experiment

  Language:R11718

• deohs/coders

  Demos, tutorials, examples, and wiki for Coding Community of Practice ("coders")

  Language:HTML91131

• FredHutch/bash-workbench

  BASH Workbench

  Language:Python957

• risqueslab/CRISPR-DS

  Analysis Pipeline for CRISPR-Duplex Sequencing data processing

  Language:Python2411

• risqueslab/DuplexSequencingScripts

  Language:Python2402

• risqueslab/MAF_analysis_template

  A MAF analysis template to be used with multi-sample MAF files in the Risques lab

  Language:R1301

• risqueslab/PolyG-DS

  CRISPR-DS with Poly_G data processing pipeline

  Language:Python140