willpitchers

willpitchers's Stars

• jtleek/datasharing

  The Leek group guide to data sharing

  6.6k566357244k

• jesseduffield/horcrux

  Split your file into encrypted fragments so that you don't need to remember a passcode

  Language:Go4.7k2823129

• pachterlab/gget

  🧬 gget enables efficient querying of genomic reference databases

  Language:Python961107175

• thackl/gggenomes

  A grammar of graphics for comparative genomics

  Language:R6321216165

• kanzure/pdfparanoia

  pdf watermark removal library for academic papers

  Language:Python535234652

• bxlab/metaWRAP

  MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis

  Language:Shell40617549190

• bacook17/acronym

  ACRONYM (Acronym CReatiON for You and Me)

  Language:Python39291231

• ParBLiSS/FastANI

  Fast Whole-Genome Similarity (ANI) Estimation

  Language:C++3831313267

• taowenmicro/EasyMicrobiomeR

  Using R language in microbiome analysis

  Language:HTML2883883

• mothur/mothur

  Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.

  Language:C++27034715110

• chklovski/CheckM2

  Assessing the quality of metagenome-derived genome bins using machine learning

  Language:Scilab184811221

• bionitio-team/bionitio

  Demonstrating best practices for bioinformatics command line tools

  Language:Shell11675126

• BGI-flexlab/SOAPnuke

  A Tool for integrated Quality Control and Preprocessing on FASTQ or BAM/CRAM files

  Language:C++104104227

• mytardis/mytardis

  MyTardis - a data management system for private lab/facility data

  Language:Python89634564

• dill/beyonce

  :crown: :bee: :bar_chart: Beyoncé colour palettes for R

  Language:R83829

• almiheenko/AGB

  Interactive visualization of assembly graphs

  Language:JavaScript807127

• 10XGenomics/supernova

  10x Genomics Linked-Read Diploid De Novo Assembler

  Language:C++6513726

• leylabmpi/Struo

  Ley Lab MetaGenome Profiler DataBase generator

  Language:Jupyter Notebook487134

• biocore/unifrac

  Language:Python39106517

• databio2022/GraphBio

  GraphBio: a shiny web app to easily perform popular visualization analysis for omics data

  Language:R3331014

• Edinburgh-Genome-Foundry/crazydoc

  Read DNA sequences from colourful Microsoft Word documents

  Language:Python32603

• mazzalab/fastqwiper

  An ensemble method to recover corrupted FASTQ files, drop or fix pesky lines, remove unpaired reads, and settle reads interleaving.

  Language:Python251243

• typhoidgenomics/genotyphi

  Assign genotypes to Salmonella Typhi genomes based on VCF files (mapped to Typhi CT18 reference genome)

  Language:Python2451010

• boulund/phaster_scripts

  Small utility script to submit genomes to PHASTER for phage detection

  Language:Python232411

• tseemann/scripts

  Miscellaneous Perl scripts from 20 years in microbial bioinformatics

  Language:Perl1710

• FischbachLab/ninjaMap

  Compute strain abundance in a defined microbial community

  Language:Python9422

• kristyhoran/Coreugate

  A simple cgMLST pipeline

  Language:Python6251

• sam-k/seq-quality-trimming

  Trimming Sanger sequencing reads by quality

  Language:Python6100

• UoM-ResPlat-DevOps/SpartanBioinformatics

  Language:HTML4604

• kviljoen/uct-srst2

  MLST using srst2, implemented in Nextflow

  Language:Nextflow3203