The Triche Lab

MTseeker

mitochondrial variant analysis tools

biscuiteer

tools for analysing Biscuit (https://huishenlab.github.io/biscuit/) output

spiky

velocessor

velocity processor

bamSliceR

Slice and dice controlled-access BAMs for thousands of samples

compartmap

Chromatin compartment inference from ATACseq, RNAseq, and DNA methylation

cropcircle

metabolomics imputation, factorization, manipulation

h5testR

simplistic package for HDF5-related testing in R/Bioconductor

spikeR

Some best practices for using spike-in controls in various single-cell and bulk assays

chromophobe

a package to handle ChromHMM (http://compbio.mit.edu/ChromHMM/) and similar segmentation models in R

plotfly

plotly automation for various dimension reduction swappage

trichelab.github.io

Organization site on github.io (supposedly)

biscuiteerData

cell-census

CELLxGENE Cell Census

enmity

loading scNMT raw(-ish) data

ExpDesign2021

A package to ensure that all dependencies are installed for Experimental Design & Biostats practical sessions. Scroll down to the README for installation details.

Fig2

Rmarkdown output

GEMLI

GEMLI fork

pluto-sdk-R

R package for interacting with the Pluto API

RcppML

Rcpp Machine Learning: Fast robust NMF, divisive clustering, and more

scGate

marker-based purification of cell types from single-cell RNA-seq datasets

Schiele

Like Seurat, but for people with less than 1024GB of RAM

scing

SCING: Single-Cell pIpeliNe Garden (pronounced as "sing" /siŋ/)

single_cell_analyses

Examples to help bootstrap your analysis of single cell data sets

singlet

Single-cell analysis with non-negative matrix factorization

sturgeon

tbmate

TabixMate: a companion tool that works with tabix to enable coordinate-date decoupling.

tbmater

tabixmate R wrapper

UMIcountR

WorldsSimplestCodeReview

The importance of replication and the unimpeachable virtues of self-correcting science