Stars
CAusal Reasoning for Network Identification with integer VALue programming in R
Parsing, Manipulation, and Visualization of Metabarcoding/Taxonomic data
Library to build command line interfaces based on Click. It extends click with: option groups, constraints (e.g. mutually exclusive params), command aliases, help themes, "did you mean ...?" sugges…
Functions for reproducibly Obtaining and Normalizing Data re-Used from Elsewhere
VIRify: detection of phages and eukaryotic viruses from metagenomic and metatranscriptomic assemblies
EcoTyper is a machine learning framework for large-scale identification of cell states and cellular ecosystems from gene expression data.
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
💌 Create simple, beautiful personal websites and landing pages using only R Markdown.
📦 🐳 Dockerfiles and documentation on tools for public health bioinformatics
🔎 💊 Mass screening of contigs for antimicrobial and virulence genes
📦 An R package for accessing genomics data from UCSC Xena platform, from cancer multi-omics to single-cell RNA-seq https://cran.r-project.org/web/packages/UCSCXenaTools/
IOBR is an R package to perform comprehensive analysis of tumor microenvironment and signatures for immuno-oncology.
Open source code for AlphaFold.
HUMAnN is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
Network construction, analysis, and comparison for microbial compositional data
MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
selbal: selection of balances for microbial signatures
Differential abundance (DA) and correlation analyses for microbial absolute abundance data
🌲 An easy-to-use and scalable toolkit for genomic alteration signature (a.k.a. mutational signature) analysis and visualization in R https://shixiangwang.github.io/sigminer/reference/index.html