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phyloseq

phyloseq is a set of classes, wrappers, and tools (in R) to make it easier to import, store, and analyze phylogenetic sequencing data; and to reproducibly share that data and analysis with others. See the phyloseq front page:

picrust

Phylogenetic Investigation of Communities by Reconstruction of Unobserved STates (PICRUST): Official repository for software and unit tests

picrust2

Code, unit tests, and tutorials for running PICRUSt2

plotrix

Lots of plots, various labeling, axis and color scaling functions.

pomashiny

:apple: Web-based User-friendly Workflow for Pre-processing and Statistical Analysis of Mass Spectrometry Data

projectils

Projection of single-cell transcriptomics data onto a reference T cell atlas

regex101

This repository is currently only used for issue tracking for www.regex101.com

ribbon

A genome browser that shows long reads and complex variants better

rna2cm

Pipeline for the identification of cancer-related mutations from RNA-seq data

rnacocktail

rnaindel

Somatic indel discovery tool for tumor RNA-Seq data.

saphire

Modelling transmission dynamics of COVID-19, while accounting for presymptomatic infectiousness, time-varying ascertainment rates, transmission rates and population movements.

sarek

Analysis pipeline to detect germline or somatic variants from WGS / targeted sequencing

sceasy

A package to help convert different single-cell data formats to each other

sceqtl

sciclone

An R package for inferring the subclonal architecture of tumors

scrublet

Detect doublets in single-cell RNA-seq data

seacr

SEACR: Sparse Enrichment Analysis for CUT&RUN

see

:art: Visualisation toolbox for beautiful and publication-ready figures

seq

A high-performance, Pythonic language for bioinformatics

sierra

Discover differential transcript usage from polyA-captured single cell RNA-seq data

sourcetracker2

SourceTracker2

ssgsea2.0

Single sample Gene Set Enrichment analysis (ssGSEA) and PTM Enrichment Analysis (PTM-SEA)

ssh

Native SSH client in R based on libssh

staar

An R package for performing STAAR procedure in whole genome sequencing studies

stream

STREAM: Single-cell Trajectories Reconstruction, Exploration And Mapping of single-cell data

tableone

R package to create "Table 1", description of baseline characteristics with or without propensity score weighting

tcga

Microbial analysis in TCGA data

tcgamutations

R data package for pre-compiled somatic mutations from TCGA cohorts (from Broad Firehose and TCGA MC3 Project)

tcr-bcr-seq-analysis

T/B cell receptor sequencing analysis notes