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programming-notes

Notes for Programming

q_lncrna_analysis

qianlab

SCRIPTS about analysis in QIANLAB

qplot

qplot

r-in-centos-7

Use R!

r_code

Some useful R code in Bioinformatics and Phylogenetics

r_for_phylogeny

My R code.

r_learn

R study related

r_phylo

My R code for sever phylogenetic computation.

resequecning_data_process

rig

An implementation of the RIG workflow

rmate

Edit files from an ssh session in TextMate

rna-seq

Automated TopHat-cuffdiff pipeline for illumina paired-end data for ran-seq data analysis

rnaseq_tutorial

Informatics for RNA-seq: A web resource for analysis on the cloud. Educational tutorials and working pipelines for RNA-seq analysis including an introduction to: cloud computing, critical file formats, reference genomes, gene annotation, expression, differential expression, alternative splicing, data visualization, and interpretation.

rphylip

An R interface for PHYLIP.

samtools-utilities

Utilities for Samtools ( http://samtools.sourceforge.net/ )

segtor

Segtor: Rapid Annotation of Genomic Coordinates and Single Nucleotide Variations Using Segment Trees.

selectiontools

Pipeline to take VCF through to Selection Analysis.

small_rna_pipeline

Start to handle the analyses of small RNA in plant

smcpp

SMC++ infers population history from whole-genome sequence data.

snphylo

A pipeline to generate a phylogenetic tree from huge SNP data

speedseq

A flexible framework for rapid genome analysis and interpretation

spyder

Official repository for Spyder - The Scientific PYthon Development EnviRonment

svpv

Structural Variant Prediction Viewer

teachingmaterial

RNA-seq data analysis practical

teanalysis

Analysis of TE contribution to features (transcripts or simple features). Includes utils to test enrichment.

telescope

Quantification of transposable element expression using RNA-seq

test_circos

textmate

TextMate is a graphical text editor for OS X 10.7+

the-art-of-command-line

Master the command line, in one page