Pinned Repositories
bioscript
BioScript-1
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
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
lran2008's Repositories
lran2008/BioScript-1
lran2008/GATK-pipeline
A shell script which implements GATK pipeline for variant calling.
lran2008/gatk_pipeline
GATK Pipeline: Recalibrates mapping qualities and calls variants using GATK
lran2008/RSEM
RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
lran2008/bioscript
lran2008/BioUtils
Python scripts for miscellaneous bioinformatics stuff.
lran2008/Chromosome-Quotient
Pipeline to identify interesting Y chromosome genes
lran2008/dotPlotly
Generate an interactive dot plot from mummer or minimap alignments
lran2008/gatk-automator
Python GUI for automating gatk analysis
lran2008/gffutils
GFF and GTF file manipulation and interconversion
lran2008/hPSMC
Tools for F1 hybrid PSMC (hPSMC) divergence time inference from whole genomes
lran2008/last
Copy of the last aligner
lran2008/liran_rnaseq
lran2008/lncrscan
Automatically exported from code.google.com/p/lncrscan
lran2008/metaRNASeq
:exclamation: This is a read-only mirror of the CRAN R package repository. metaRNASeq — Meta-analysis of RNA-seq data
lran2008/metaSeq
Meta-analysis package for RNA-seq count data
lran2008/metaseqr
An R package for the analysis, meta-analysis and result reporting of RNA-Seq gene expression data
lran2008/mGSV
Multiple Genome Synteny Viewer
lran2008/NextDenovo
Fast and accurate de novo assembler for third generation sequencing (TGS) reads
lran2008/Perl-for-Bioinformatics
An attempt to help anyone interested in using Perl for Bioinformatics
lran2008/PiNSiR
Pi_N and Pi_S estimation from NGS data using R
lran2008/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)
lran2008/psmc
Implementation of the Pairwise Sequentially Markovian Coalescent (PSMC) model
lran2008/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.
lran2008/RNA-seq-scripts
This is a collection of small scripts built by the Lenz lab to make RNA sequencing tasks more efficient.
lran2008/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.
lran2008/seqscripts
Scripts for parsing the output from the Tophat/Cufflinks/Cuffcompare pipeline into other formats and analyzing and editing GTF files.
lran2008/smcrun
Managing and running psmc/msmc with data and simulations