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p1_02_differentialmethylation

Probe-wise differential methylation analysis using glmmTMB for 5mC and gamlss for 5hmC

p1_04_dmrcate-annotation

P1 methylation data processing DMRcate, network analysis and annotation

pames

Tool to estimate purity of tumor samples exploiting DNA Methylation data

pare

PARE: a computational method to Predict Active Regulatory Elements

pba

Population balance analysis

platetools

An R package for plotting 96 / 384 / 1536 well plates

powerlawgraph

Implementation for the paper "Bayesian inference on random simple graphs with power-law degree distributions"

pyinseq

Python pipeline for analyzing INSeq Insertion Sequencing data

qdnaseq

QDNAseq package for Bioconductor

qdnaseq_bin_annotations

This repo contains bin annotations for QDNAseq CNA calling

r-ecology

Data Carpentry R lessons on ecology

readdepth

R package for inferring copy number from read depth

rtd_docs

Repo containing docs for readthedocs

sample_data

Repo containing test/sample data for analysis (quick)

scanorama

Panoramic stitching of heterogeneous single cell transcriptomic data

scatac_compartments

A/B compartments from single-cell ATAC seq (scATAC)

scater

Clone of the Bioconductor repository for the scater package, see https://bioconductor.org/packages/devel/bioc/html/scater.html for the official development version.

scm3c-seq

seqspec

singlecellmultimodal

Single Cell multimodal data scripts for downloading datasets

sparsematrixutils

Small utility package to work with sparse matrices in R

sparta-teaching

Teaching bacterial RNA-seq with SPARTA

sparta_docs_and_tutorial

SPARTA documentation and tutorials

sparta_docs_and_tutorial-1

sparta_linux

sparta_mac

sparta_windows

sphyr

Single-cell Phylogeny Reconstruction

spiky

stream

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