brentp

450k-analysis-guide

A Practical (And Opinionated) Guide To Analyzing 450K Data

pybloomfaster

fast bloomfilter

methylcode

Alignment and Tabulation of BiSulfite Treated Reads

aclust

streaming, flexible agglomerative clustering

agoodle

numpy + GDAL == agoodle

fastahack-python

cython wrapper to fastahack

gobe

a fast, interactive, light-weight, customizable, web-based comparative genomics viewer with simple text input format.

bowfast

run bowtie then bfast on colorspace reads.

crystal

find clusters and model correlated data from DNA methylation and other genomic sources.

clustermodel

fitting models to clustered correlated data

find_cns

find conserved non-coding sequences (CNS)

shuffler

shuffle genome regions to determine probability of user-defined metric

4bit

4bit fasta format.

bioawk

BWK awk modified for biological data

flatfeature

python module for dealing with BED format for genomic data as a numpy array.

pybedtools

Python wrapper -- and more -- for Aaron Quinlan's BEDTools (bioinformatics tools)

tabix-py

interface to tabix using cffi

bedtools-python

A Python interface to the BEDTools API using Cython

cysolar

copy of pysolar using cython

dotfiles

my .bash, .vim, .* files

pyfastx

unified access to fasta, fastx using kseq.h + ??

brentp.github.com

clustermodelr

fit models to clustered, correlated data (R package)

fixle

fast, fixed-length, integer-keyed db via tokyo-cabine

pyfaidx

"samtools faidx" compatible FASTA indexing in pure python

synstats

code for synstats.appspot.com

totable

simple python / cython wrapper to tokyo cabinet tables

bedtools

A powerful toolset for genome arithmetic.

bootstrip

Resampling residuals of a linear model to determine significance with bootstrap-like sub-sampling

rstuff

R stuff I wrote