Notebook, data and Dash app used in talk on visualisation libraries

utility functions for analyzing 10X genomics data

Tools for analyzing 10X Genomics data

TransDecoder source

Reconstructing Three-Dimensional Chromosomal Structures from Hi- C Interaction Frequency Data using Distance Geometry Simulated Annealing

Effective Computing—Resources for Computational Biologists

Utility functions to work with output from the HOMER motif finding program

📚 Freely available programming books

TADbit is a complete Python library to deal with all steps to analyze, model and explore 3C-based data. With TADbit the user can map FASTQ files to obtain raw interaction binned matrices (Hi-C like…

“When everything is connected to everything else, for better or worse, everything matters.” Bruce Mau

🌈Scaffold genome sequence assemblies using linked or long read sequencing data

A cool place to store your Hi-C

Linked-Read Alignment Tool

The BioPerl Web site: http://bioperl.org

A set of pipelines for Hi-C and ChIP-Seq analysis.

Repository of the 3PD tool: Rapid design of optimal primers for chromosome conformation capture assays

SRA Tools

🔬 Assemble large genomes using short reads

Scripts for bioinformatics data processing and analysis

🔬 Path to a free self-taught education in Bioinformatics!

Tools for bioinformatics moved to http://git.genenetwork.org/pjotrp/bioinformatics

Validated, scalable, community developed variant calling, RNA-seq and small RNA analysis

Useful bash one-liners for bioinformatics.

CoGe (Comparative Genomics) Platform

RetroSeq is a bioinformatics tool that searches for mobile element insertions from aligned reads in a BAM file and a library of reference transposable elements. Please read the wiki page (link belo…

EDGE is a highly adaptable bioinformatics platform that allows laboratories to quickly analyze and interpret genomic sequence data.

Biopieces is a bioinformatic framework of tools easily used and easily created.

Minimal examples of data structures and algorithms in Python