Brent Pedersen (brentp)

brentp

Geek Repo

Company:University of Utah

Location:Utrecht, The Netherlands

Twitter:@brent_p

Github PK Tool:Github PK Tool


Organizations
quinlan-lab

Brent Pedersen's repositories

450k-analysis-guide

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

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methylcode

Alignment and Tabulation of BiSulfite Treated Reads

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aclust

streaming, flexible agglomerative clustering

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agoodle

numpy + GDAL == agoodle

fastahack-python

cython wrapper to fastahack

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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.

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clustermodel

fitting models to clustered correlated data

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find_cns

find conserved non-coding sequences (CNS)

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shuffler

shuffle genome regions to determine probability of user-defined metric

4bit

4bit fasta format.

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bioawk

BWK awk modified for biological data

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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)

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tabix-py

interface to tabix using cffi

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bedtools-python

A Python interface to the BEDTools API using Cython

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cysolar

copy of pysolar using cython

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dotfiles

my .bash, .vim, .* files

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learnflash

all the stuff i want to remember how to do in haxe / flash

pyfastx

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

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clustermodelr

fit models to clustered, correlated data (R package)

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fixle

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

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pyfaidx

"samtools faidx" compatible FASTA indexing in pure python

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synstats

code for synstats.appspot.com

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totable

simple python / cython wrapper to tokyo cabinet tables

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bedtools

A powerful toolset for genome arithmetic.

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bootstrip

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

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rstuff

R stuff I wrote

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