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ncbi_taxonomy

A python program to query the NCBI taxonomy tree. This code is now UNMAINTAINED, as it has been integrated in the ETE toolkit (http://github.com/jhcepas/ete)

networkd3

D3 JavaScript Network Graphs from R

neural-networks-and-deep-learning

Code samples for my book "Neural Networks and Deep Learning"

onco_lnc

opencl-book-samples

Automatically exported from code.google.com/p/opencl-book-samples

opencv

Open Source Computer Vision Library

parse-kegg

Script to format KEGG pathway data for PathScan

parsertomallet

pattern_classification

A collection of tutorials and examples for solving and understanding machine learning and pattern classification tasks

pero_transcriptome

ph525x

ph525x. functions only, no data

picard

A set of tools (in Java) for working with next generation sequencing data in the BAM (http://samtools.github.io/hts-specs) format.

pindel

Pindel can detect breakpoints of large deletions, medium sized insertions, inversions, tandem duplications and other structural variants at single-based resolution from next-gen sequence data. It uses a pattern growth approach to identify the breakpoints of these variants from paired-end short reads.

pindel2

Detecting break points of large deletions and medium sized insertions from paired-end short read

polyscape

Homopolymer and microsatellite analysis tool

practical-machine-learning

Notes and code from Practical Machine Learning course slides

proyecto-titulacion

Sistema generador de diferentes series de instrumentos de evaluación para la Coordinación de Fundamentos de Computación y Programación de la Universidad de Santiago de Chile

python_reference

Useful functions, tutorials, and other Python-related things

qsub-omics

Functions to qsub common genomics and transcriptomics tools, including genome and transcriptome assembly and annotation

r-cancr

The cancR package. Will be a collection of useful helper functions.

r-parallel

Using R with many CPUs

raffairsdataanalysis

Exploratory data analysis on the R Affairs data set

rap-green

Automatically exported from code.google.com/p/rap-green

rbootcamp2015

Materials for the Hunter / CUNY School of Public Health R Bootcamp 2015

regulomeexplorer

rtcgatoolbox

scikit-learn.github.io

Scikit-learn website hosted by github

seqpeek

SeqPeek Visualization

smartas

📓Notebook of Climente-González et al. (2017), The Functional Impact of Alternative Splicing in Cancer.

somatic-benchmark

Tools for comparing somatic variant calling tools.