Repositories list

• protocols

  Public
  A repository for the protocols and guides used in Dr. Eric Vallender's lab.

  TeX

  •

  Other

  •1•0•27•0•Updated Oct 19, 2024Oct 19, 2024

• MicrobiomeR

  Public
  A comprehensive and customizable R package for microbiome analysis.

  bioinformaticscolor-palettemetagenomics+ 14beta-diversitymicrobial-genomicsmicrobiologymicrobiomepcoamicrobiome-analysisphyloseq+ 7

  R

  •

  MIT License

  •4•21•17•0•Updated Dec 9, 2022Dec 9, 2022

• vallenderlab.github.io

  Public
  This is the software website for the Vallender Lab.

  JavaScript

  •

  MIT License

  •0•0•3•0•Updated Dec 7, 2022Dec 7, 2022

• mgap

  Public
  apinhpmgap

  Python

  •

  MIT License

  •0•0•1•0•Updated Jul 6, 2020Jul 6, 2020

• mu-paper-dataviz

  Public
  Data visualization for Xiao's mu opiod paper.

  R

  •0•0•1•0•Updated May 2, 2020May 2, 2020

• fastStructure

  Public
  A variational framework for inferring population structure from SNP genotype data.

  Python

  •

  MIT License

  •51•0•0•0•Updated Jan 7, 2020Jan 7, 2020

• rnaseq-tuxedo-suite

  Public
  An RNASeq snakemake workflow using the Tuxedo suite.

  snakemakerna-seq-snakemakerna-seq-pipeline+ 3snakemake-workflowrnaseq-tuxedornaseq-pipeline

  Python

  •

  MIT License

  •1•0•0•0•Updated Aug 19, 2019Aug 19, 2019

• dnaseq-gatk-variant-calling

  Public
  A DNA sequencing pipeline based on the GATK best-practices workflow.

  Python

  •

  MIT License

  •0•0•0•0•Updated Jul 25, 2019Jul 25, 2019

• cookiecutter-snakemake-workflow

  Public
  A cookiecutter for snakemake workflows.

  snakemakecookiecuttersnakemake-workflow

  Python

  •

  MIT License

  •0•0•0•0•Updated May 2, 2019May 2, 2019

• snakemake-tutorial

  Public
  0•0•0•0•Updated May 1, 2019May 1, 2019

• vallender-pkgdown-theme

  Public
  A css theme for Vallender Lab pkgdown documentation.

  cssthemepkgdown

  CSS

  •

  MIT License

  •0•1•1•0•Updated Mar 27, 2019Mar 27, 2019

• MicrobiomeR-JOSS

  Public
  This repository hosts our JOSS journal article for the MicrobiomeR package.

  joss

  TeX

  •0•0•0•0•Updated Mar 21, 2019Mar 21, 2019

• semver.org

  Public
  Semantic Versioning spec and website

  CSS

  •284•0•0•0•Updated Dec 3, 2018Dec 3, 2018

• workflowr-tutorial

  Public
  workflowr

  MIT License

  •0•0•0•0•Updated Nov 13, 2018Nov 13, 2018

• JournalAnalysis

  Public
  A repository for exploring journals that we would like to publish under.

  jstorjournal-analysisscimago

  R

  •0•2•6•0•Updated Sep 11, 2018Sep 11, 2018

• vcf_to_dataframe

  Public
  Get a pandas DataFrame from a possibly gzipped VCF file.

  Python

  •2•0•0•0•Updated Mar 9, 2018Mar 9, 2018