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bseqsc

Bulk-Sequence Single-Cell Gene Expression Deconvolution Pipeline

cellbender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

celltrails

Mirror of the Bioconductor package CellTrails (http://bioconductor.org/packages/CellTrails/)

chip-seq-analysis

ChIP-seq analysis notes from Ming Tang

chip-seq-pipeline2

chipseq

ChIP-seq peak-calling, QC and differential analysis pipeline (Snakemake port of the nextflow pipeline at https://nf-co.re/chipseq).

chromvar

chromatin Variability Across Regions (of the genome!)

cite-seq-count

A tool that allows to get UMI counts from a single cell protein assay

clickme

An R package to create interactive plots

clipper

A tool to identify CLIP-seq peaks

coloc-tesseler

complexheatmap

Make Complex Heatmaps

cosmosr

crisprseq

A pipeline for the analysis of CRISPR edited next generation sequencing (NGS) data. CRISPR gene knockouts (KO), CRISPR knock-ins (KI), base editing (BE) and prime editing (PE) experiments

crossmap

CrossMap is a python program to lift over genome coordinates from one genome version to another.

cytoscape-tutorials

Collection of modular Cytoscape tutorials for online presentation using reveal.js

dalex

Descriptive mAchine Learning EXplanations

dapars

DaPars(Dynamic analysis of Alternative PolyAdenylation from RNA-seq)

dat

:floppy_disk: peer-to-peer sharing & live syncronization of files via command line

deep-learning-keras-tensorflow

Introduction to Deep Neural Networks with Keras and Tensorflow

deep-learning-with-r-notebooks

R notebooks for the code samples of the book "Deep Learning with R"

deeplearning-biology

A list of deep learning implementations in biology

deltasvm

Codes to run deltaSVM models to predict allelic TF binding

dna-seq-gatk-variant-calling

This Snakemake pipeline implements the GATK best-practices workflow

dna-seq-varlociraptor

Variant detection with Delly and Freebayes, followed by statistical assessment with Varlociraptor

docopt.r

Command-line interface description language for R (http://docopt.org)

doing-bayesian-data-analysis-in-brms-and-the-tidyverse

The bookdown version lives here: https://bookdown.org/content/3686

dorothea

R package to access DoRothEA's regulons

downloader

Easy & parallel download of FASTQ files from public repositories

drop-seq

Java tools for analyzing Drop-seq data