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midas

An integrated pipeline for estimating strain-level genomic variation from metagenomic data

midas2_scripts

Scripts for MIDAS2 (Metagenomic Intra-Species Diversity Analysis System 2)

midas2nv

Metagenomic Intra-Species Diversity Analysis 2 using GPU

misc

Miscellaneous data for the package

nmfbina

Non-Negative Matrix Factorization for Binary Data

nvbio

NVBIO is a library of reusable components designed to accelerate bioinformatics applications using CUDA.

piphir

Functional prediction from 16S rRNA gene sequencing data using Piphillin algorithm in R

pubmedmini

Storing PMC article information for each gene query

pykegg

Analyze and visualize KEGG information using network approach

q2-pathway

QIIME 2 plugin for analyzing biological pathway information based on gene family abundances

rigraph

igraph R package

screpertoire

A toolkit for single-cell immune profiling

scstruc

Gene regulatory network based on Bayesian network structure in single-cell transcriptomics

seqtk

Toolkit for processing sequences in FASTA/Q formats

sh

sh color palette

singlecellthoughts

Assorted thoughts, explanations and justifications for code in the scran package and the simpleSingleCell workflow.

sjrdataplot

Inspect SJR data by Shiny application

software

stana

Metagenotyping analysis in R

textora

over representation analysis for the gene description

tidybn

Tidy manipulation of Bayesian network

tidygraph

A tidy API for graph manipulation

tidyseurat

Seurat meets tidyverse. The best of both worlds.

tidysinglecellexperiment

Brings SingleCellExperiment objects to the tidyverse

tidysummarizedexperiment

Brings SummarizedExperiment to tidiverse with no side-effects