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2020-epigenetics_workshop

ATAC-Seq, ChIP-Seq, and whole genome bisulfite! An introduction to analyzing some of the most popular types of epigenetic data.

agptools

Tools for working with agp files

ampliconarchitect

AmpliconArchitect (AA) is a tool to identify one or more connected genomic regions which have simultaneous copy number amplification and elucidates the architecture of the amplicon.

arriba

Fast and accurate gene fusion detection from RNA-Seq data

awesome-programming-books

📚 A curated list of awesome programming books (Algorithms and data structures, Artificial intelligence, Software Architecture, Human–computer interaction, Operating Systems, Database Systems, IT Security, Concurrency, Interpreters and Compilers, High-Performance Computing, Distributed Systems, Game Development, Mathematical optimization)

binf511

bioinformatics-workbook

Bioinformatics Workbook repository

bioinfotools

Documenting usage and experience with bioinformatic tools

biotutorials

Tutorial Notebooks of BioJulia

bisbee

alternative splicing analysis pipeline

bwa-mem2

The next version of bwa-mem

canu

A single molecule sequence assembler for genomes large and small.

caveman

Causal Variant Evidence Mapping with Non-parametric resampling

ccscheck

Evaluate quality, model fit, QV calibration and all else CCS

cfdna-wgs-manuscript-code

Code used to generate the results in "Somatic chronology of treatment-resistant prostate cancer via deep whole-genome ctDNA sequencing"

chip-seq-analysis

ChIP-seq analysis notes from Ming Tang

chord

An R package for predicting HR deficiency from mutation contexts

chromosomer

A reference-assisted assembly tool for producing draft chromosome sequences.

clpipe

Python pipeline for neuroimaging data

cnv_sv-visualisation

Visualise copy-number alterations and structural variants

codex

Image processing software for CODEX: driftcompensation, deconvolution, uploading and segmentation

cossa-workflows

CoSSA (Prodhomme et al., 2019) is a set of workflows used to identify quickly and efficiently haplotype specific SNPs linked to a trait of interest from Whole Genome Sequencing data. All the contributors to the design of these workflows are Danny Esselink, Charlotte Prodhomme and Theo Borm (Wageningen University UR Plant Breeding).

creative-clock

Plan your day, and visually see how you spend your time.

crossmap

fork CrossMap

deeptools

Tools to process and analyze deep sequencing data.

dna-seq-analysis

DNA sequencing analysis notes from Ming Tang

dysgu

dysgu-SV is a collection of tools for calling structural variants using short or long reads

ebi_cancer_workshop_cnv

hands-on for NGS/SNParray CNV call trainning

esquisse

RStudio add-in to make plots with ggplot2

evo

DNA foundation modeling from molecular to genome scale