Pinned Repositories
adjustText
A small library for automatically adjusting text position in matplotlib plots to minimize overlaps.
Auto-Escher-map-for-CobraPy
Tool for generating an Escher map of a Cobra metabolic model
biopython.github.io
Source of biopython.org website, migrated from MediaWiki
bioscreen
Classes and utils for exploration of biological screen data - proteomics, RNA-seq, CRISPR screens and the like.
BlastScoreRatio
Python scripts to calculate and visualise the Blast Score Ratio of amino acid sequences. BSR reference: Rasko, D. A., Myers, G. S., & Ravel, J. (2005). Visualization of comparative genomic analyses by BLAST score ratio. BMC bioinformatics, 6(1), 2.
crispr_screen_viewer
Take output of mageck and drugz to produce interactive Dash charts.
crispr_tools
Tools for analysing CRISPR screens
gene_name_updater
Update gene symbols from HGNC and Entrez databases.
interproscantools
Run and tabulate results of batch Interproscan
keepadapt
This version of cutadapt removes sequences before/after adapters.
johncthomas's Repositories
johncthomas/crispr_screen_viewer
Take output of mageck and drugz to produce interactive Dash charts.
johncthomas/Auto-Escher-map-for-CobraPy
Tool for generating an Escher map of a Cobra metabolic model
johncthomas/BlastScoreRatio
Python scripts to calculate and visualise the Blast Score Ratio of amino acid sequences. BSR reference: Rasko, D. A., Myers, G. S., & Ravel, J. (2005). Visualization of comparative genomic analyses by BLAST score ratio. BMC bioinformatics, 6(1), 2.
johncthomas/keepadapt
This version of cutadapt removes sequences before/after adapters.
johncthomas/adjustText
A small library for automatically adjusting text position in matplotlib plots to minimize overlaps.
johncthomas/biopython.github.io
Source of biopython.org website, migrated from MediaWiki
johncthomas/bioscreen
Classes and utils for exploration of biological screen data - proteomics, RNA-seq, CRISPR screens and the like.
johncthomas/crispr_tools
Tools for analysing CRISPR screens
johncthomas/easybuild-easyconfigs
A collection of easyconfig files that describe which software to build using which build options with EasyBuild.
johncthomas/gene_name_updater
Update gene symbols from HGNC and Entrez databases.
johncthomas/interproscantools
Run and tabulate results of batch Interproscan
johncthomas/fuzzymatching
Map fixed length sequences from one file to uniquely closest sequence in another file, using Levenshtein distance.
johncthomas/GoGameOfLife
Conway's game of life in Go, a practice thing
johncthomas/JACKS_old
johncthomas/jacks_tools
Post-processing tools for JACKS (felicityallen/JACKS).
johncthomas/jttools
Useful things.
johncthomas/off_target_prediction
johncthomas/picklepot
johncthomas/shiftES
Implimentation of Wilcox shift effect size with command line interface
johncthomas/wgbs_tools
tools for working with Bisulfite Sequencing data while preserving reads intrinsic dependencies