lran2008

BioScript-1

GATK-pipeline

A shell script which implements GATK pipeline for variant calling.

gatk_pipeline

GATK Pipeline: Recalibrates mapping qualities and calls variants using GATK

RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data

bioscript

BioUtils

Python scripts for miscellaneous bioinformatics stuff.

Chromosome-Quotient

Pipeline to identify interesting Y chromosome genes

dotPlotly

Generate an interactive dot plot from mummer or minimap alignments

gatk-automator

Python GUI for automating gatk analysis

gffutils

GFF and GTF file manipulation and interconversion

hPSMC

Tools for F1 hybrid PSMC (hPSMC) divergence time inference from whole genomes

last

Copy of the last aligner

liran_rnaseq

lncrscan

Automatically exported from code.google.com/p/lncrscan

metaRNASeq

:exclamation: This is a read-only mirror of the CRAN R package repository. metaRNASeq — Meta-analysis of RNA-seq data

metaSeq

Meta-analysis package for RNA-seq count data

metaseqr

An R package for the analysis, meta-analysis and result reporting of RNA-Seq gene expression data

mGSV

Multiple Genome Synteny Viewer

NextDenovo

Fast and accurate de novo assembler for third generation sequencing (TGS) reads

Perl-for-Bioinformatics

An attempt to help anyone interested in using Perl for Bioinformatics

PiNSiR

Pi_N and Pi_S estimation from NGS data using R

piper

A genomics pipeline build on top of the GATK Queue framework. Main repository: https://github.com/NationalGenomicsInfrastructure/piper (make sure you fork from there)

psmc

Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model

RNA-seq-Graph

RNA-seq Graph Builder is a method to reconstruct the Isoform Graph of a gene from RNA-seq data, without the genome information, where such a graph is a representation of the variants of alternative splicing of the gene structure.

RNA-seq-scripts

This is a collection of small scripts built by the Lenz lab to make RNA sequencing tasks more efficient.

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.

seqscripts

Scripts for parsing the output from the Tophat/Cufflinks/Cuffcompare pipeline into other formats and analyzing and editing GTF files.

smcrun

Managing and running psmc/msmc with data and simulations