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bio_tools

my libraries for comp bio

biopython

Official git repository for Biopython (converted from CVS)

biopython-notebook

Notebooks to introduce biopython

biopython.github.io

Source of biopython.org website, migrated from MediaWiki

biopython_workshop

A basic introduction to Biopython, intended for a classroom based workshop

bioruby-faster

A fast and simple parser for Fasta / FastQ files

bioruby-pipengine

A simple launcher for complex biological pipelines

biostan

Materials for BioC-2016 workshop entitled "Introduction to Bayesian Inference using Stan with Applications to Cancer Genomics"

blast

Find homologs and ident values from an inputted list of genes

bnmf

empirical Bayesian NMF for mutational signature discovery

boincstats

BOINC Hourly Statistics for Users

bowtie2

A fast and sensitive gapped read aligner

bptd_genetics

Bayesian probabilistic tensor decomposition for gene expression, combined with genetic analysis.

brass

Breakpoints via assembly - Identifies breaks and attempts to assemble rearrangements.

breakmer

A method to identify structural variation from sequencing data in target regions

breast-cancer-classification

Classify cells as benign or malignant based on cell nucleus features

brisbane2016

Workshop and talk for Brisbane, 2016 Bioc Asia meeting

browserheatmap

An interactive d3 heatmap created from, and interactive with, an R session

bsub

python wrapper to submit jobs to bsub (and later qsub)

bsubtilis_abm

Multi-scale agent-based model of competence phenotype in Bacillus subtilis

bugbase

bunny-logs

Simple log file analysis, with support for Dataflow.

burntrees

Perl scripts for manipulating output from phylogenetic MCMC software (MrBayes, BEAST)

bwa

Burrow-Wheeler Aligner for pairwise alignment between DNA sequences

campbell_et_al

Recombination maps from Campbell et al., Nat Comms, 2015

canalization

Manuscript: Canalization of the evolutionary trajectory of the human influenza virus

cancercelllines

A framework for analysing public domain cancer cell line data and integrating it with proprietary compound screening data

cancermutationhotspots

Detecting mutation hotspots in cancer genomes

cancerseqstudy

Analysis of statistical power and false positives for cancer exome sequencing studies

canopy

Accessing Intra-Tumor Heterogeneity and Tracking Longitudinal and Spatial Clonal Evolutionary History by Next-Generation Sequencing.