madsheilskov

madsheilskov's Stars

• maxanes/Feature-Extraction-Workflow-for-Target-Mutation-Selection

  Bioinformatics pipeline for the extraction of all tumor features necessary for selection of clonal mutations from whole-exome sequencing (WES) data in tumor normal settings

  Language:Python1

• MOMA-CRC/ddanalyzor

  Analysis of ddPCR raw data

  Language:R4

• adamewing/bamsurgeon

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

  Language:Python23086

• genome/bam-readcount

  Count bases in BAM/CRAM files

  Language:CMake29896

• Hogfeldt/ctDNAtool

  A software for creating and manipulating statistics from cfDNA data

  Language:Python42

• 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:Cython773274

• pughlab/ConsensusCruncher

  ConsensusCruncher is a tool that suppresses errors in next-generation sequencing data by using unique molecular identifiers (UMIs) to amalgamate reads derived from the same DNA template into a consensus sequence.

  Language:Jupyter Notebook2110

• msiemens/tinydb

  TinyDB is a lightweight document oriented database optimized for your happiness :)

  Language:Python6.7k530

• gerstung-lab/deepSNV

  The official repository for the deepSNV bioconductor packages. Branch master tracks the official Bioconductor development branch.

  Language:R146

• fulcrumgenomics/fgbio

  Tools for working with genomic and high throughput sequencing data.

  Language:Scala30867

• gwforg/gwf

  A flexible, pragmatic workflow tool.

  Language:Python3112

• Gromgorgel/ddPCR

  Digital PCR Analysis Algorithms

  Language:R74

• crazyhottommy/bioinformatics-one-liners

  Bioinformatics one liners from Ming Tang

  451130

• mailund/ctib

  Lecture notes and material for Computational Thinking in Bioinformatics

  Language:Jupyter Notebook82

• nathan-russell/hashmap

  Faster hash maps in R

  Language:C++809

• eddelbuettel/littler

  A scripting and command-line front-end for GNU R

  Language:R30850

• docopt/docopt.R

  Command-line interface description language for R (http://docopt.org)

  Language:R20820

• alimanfoo/pysamstats

  A fast Python and command-line utility for extracting simple statistics against genome positions based on sequence alignments from a SAM or BAM file.

  Language:Python18943

• dkoboldt/varscan

  Variant calling and somatic mutation/CNV detection for next-generation sequencing data

  15234

• NickSto/dunovo

  WARNING: this repo is no longer updated. Main development has moved to:

  Language:Python18

• OpenGene/AfterQC

  Automatic Filtering, Trimming, Error Removing and Quality Control for fastq data

  Language:Python20451

• CGATOxford/UMI-tools

  Tools for handling Unique Molecular Identifiers in NGS data sets

  Language:Python479189

• ARUP-NGS/BMFtools

  Barcoded Molecular Families

  Language:C++228

• galaxyproject/dunovo

  Reference-free duplex sequencing pipeline.

  Language:Python186

• xuchang116/smCounter

  smCounter: a versatile UMI-aware variant caller to detect both somatic and germline SNVs and indels. Published in article "Detecting very low allele fraction variants using targeted DNA sequencing and a novel molecular barcode-aware variant caller", BMC Genomics, 2017 18:5. https://bmcgenomics.biomedcentral.com/articles/10.1186/s12864-016-3425-4

  Language:Python206

• GalliumOS/galliumos-distro

  Docs, issues, and artwork sources for GalliumOS

  34811

• libnano/primer3-py

  Simple oligo analysis and primer design

  Language:C15642

• quwubin/MFEprimer-2.0

  MFEprimer-2.0: A fast thermodynamics-based program for checking PCR primer specificity

  Language:Python3717

• GTseq/GTseq-Pipeline

  A series of perl and python scripts for generating genotypes from NGS fastq files from GTseq library sequencing.

  Language:Perl1714

• Kennedy-Lab-UW/Duplex-Sequencing

  Language:Python5734