Repositories list

• bfx-workshop

  Public
  A course on genomics and bioinformatics from WU

  bioinformaticsdatavizgenomics+ 11analysisbiologysequencingdnaalignmentrnaseqrna+ 4

  HTML

  •19•59•0•0•Updated Dec 2, 2024Dec 2, 2024

• qc-analysis-pipeline

  Public
  Workflow used for WGS/WES data QC

  WDL

  •

  BSD 3-Clause "New" or "Revised" License

  •45•8•9•0•Updated Oct 16, 2024Oct 16, 2024

• analysis-workflows

  Public
  Open workflow definitions for genomic analysis from MGI at WUSM.

  Common Workflow Language

  •

  MIT License

  •57•102•74•15•Updated Jun 26, 2024Jun 26, 2024

• UR

  Public
  Rich Transactional Objects for Perl

  Perl

  •

  Other

  •12•3•8•4•Updated Jun 15, 2024Jun 15, 2024

• snvstory

  Public
  Rapid and accurate ancestry inference using SNVs.

  Python

  •

  BSD 3-Clause "New" or "Revised" License

  •8•0•0•0•Updated May 8, 2024May 8, 2024

• cig-pipelines

  Public
  Workflows and resources for running pipelines for somatic mutation discovery in pangenomes plus miscellaneous tools..

  WDL

  •1•0•0•0•Updated Apr 19, 2024Apr 19, 2024

• spectacle

  Public
  Ruby

  •2•0•9•9•Updated Mar 25, 2024Mar 25, 2024

• genome

  Public
  Core modules used by the GMS

  Perl

  •

  GNU Lesser General Public License v3.0

  •57•64•9•0•Updated Mar 13, 2024Mar 13, 2024

• cle-myeloseqhd

  Public
  Python

  •4•2•3•0•Updated Dec 20, 2023Dec 20, 2023

• sciclone

  Public
  An R package for inferring the subclonal architecture of tumors

  R

  •

  Other

  •55•117•4•1•Updated Oct 13, 2023Oct 13, 2023

• scrna_mutations

  Public
  Supplementary data for Petti, et al 2019 scRNA mutation publication

  Python

  •13•16•1•0•Updated Feb 1, 2023Feb 1, 2023

• docker-samtools-cwl

  Public
  Dockerfile

  •2•1•0•0•Updated Jan 24, 2023Jan 24, 2023

• docker-samtools

  Public
  Docker container for Samtools

  2•0•0•0•Updated Jan 11, 2023Jan 11, 2023

• AGFusion

  Public
  Python package to annotate and visualize gene fusions.

  Python

  •

  MIT License

  •25•4•0•0•Updated Dec 15, 2022Dec 15, 2022

• docker-mapq0-filter

  Public
  filter a vcf for variants with high percentage of mapq0 reads

  Python

  •2•0•0•0•Updated Oct 26, 2022Oct 26, 2022

• cle

  Public
  Repo for cle related software

  WDL

  •1•1•0•0•Updated Oct 19, 2022Oct 19, 2022

• docker-immuno_tools-cwl

  Public
  Shell

  •0•0•7•0•Updated Aug 23, 2022Aug 23, 2022

• bmm

  Public
  R package that uses a variational Bayesian approach to fitting a mixture of Beta distributions

  R

  •

  Other

  •9•4•2•0•Updated Aug 1, 2022Aug 1, 2022

• docker-cnvkit

  Public
  Dockerfile

  •3•0•0•0•Updated May 25, 2022May 25, 2022

• docker-fastqc-cwl

  Public
  Dockerfile

  •0•0•0•0•Updated May 25, 2022May 25, 2022

• fpfilter-tool

  Public
  Perl

  •21•6•0•1•Updated Apr 27, 2022Apr 27, 2022

• docker-vep_helper-cwl

  Public
  Perl

  •3•0•1•0•Updated Apr 5, 2022Apr 5, 2022

• docker-somatic-llr-filter

  Public
  Container for the somatic-llr filter

  Python

  •2•0•0•0•Updated Mar 11, 2022Mar 11, 2022

• hic-pipeline

  Public
  HiC uniform processing pipeline

  WDL

  •

  MIT License

  •24•0•0•0•Updated Feb 4, 2022Feb 4, 2022

• bam-readcount

  Public
  Count bases in BAM/CRAM files

  CMake

  •

  MIT License

  •95•306•51•0•Updated Jan 31, 2022Jan 31, 2022

• qc-metric-aggregator

  Public
  Given the output directory of a QC pipeline and a threshold config file, parse out the desired metrics and evalute them against the thresholds.

  Python

  •

  MIT License

  •2•1•5•0•Updated Nov 4, 2021Nov 4, 2021

• cle-myeloseq

  Public
  Repo for cle myeloseq/haloplex assay

  Perl

  •1•1•0•0•Updated Oct 8, 2021Oct 8, 2021

• docker-bam-readcount

  Public
  Docker containerization for "bam-readcount"

  Dockerfile

  •4•0•0•1•Updated Oct 8, 2021Oct 8, 2021

• docker-bam_readcount_helper-cwl

  Public
  Python

  •9•3•2•1•Updated Jul 8, 2021Jul 8, 2021

• docker-homer

  Public
  fork of the quay.io homer image, moving annotations to my hardcoded link

  Dockerfile

  •4•0•0•0•Updated Jun 11, 2021Jun 11, 2021