Tools   Select Another Resource Report Type

http://sourceforge.net/projects/ec2kegg/

A perl-based package to perform comparative analysis of metabolic pathways between two organisms.

Proper citation: EC2KEGG (RRID:SCR_012127) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cnvcapseq/

Software for accurate and sensitive CNV discovery and genotyping in long-range targeted resequencing.

Proper citation: cnvCapSeq (RRID:SCR_012126) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ealps/

Software that uses the genotype data in conjunction with the pooled sequence data in order to accurately estimate the proportions of the samples in the pool, even in cases where not all individuals in the pool were genotyped (eALPS-LD).

Proper citation: eALPS (RRID:SCR_012130) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/plek/

An alignment-free software tool which uses a computational pipeline based on an improved k-mer scheme and a support vector machine (SVM) algorithm to distinguish lncRNAs from messenger RNAs (mRNAs), in the absence of genomic sequences or annotations. It is especially suitable for PacBio or 454 sequencing data and large-scale transcriptome data.

Proper citation: PLEK (RRID:SCR_012132) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/ldx/

A computational software tool for estimating linkage disequilibrium (LD) from pooled resequencing data.

Proper citation: LDx (RRID:SCR_012131) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/reditools/

A suite of python scripts to perform high-throughput investigation of RNA editing using next-generation sequencing data.

Proper citation: REDItools (RRID:SCR_012133) Copy   

•   Source: SciCrunch Registry

http://pprospector.sourceforge.net/

A pipeline of software programs to design and analyze PCR primers. It is built in Python using the open-source PyCogent toolkit.

Proper citation: PrimerProspector (RRID:SCR_012136) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/icelogo/

Software that builds on probability theory to visualize significant conserved sequence patterns in multiple peptide sequence alignments against background (reference) sequence sets that can be tailored to the studied system and the used protocol.

Proper citation: iceLogo (RRID:SCR_012137) Copy   

•   Source: SciCrunch Registry

http://musite.sourceforge.net/

A Java-based standalone application for predicting both general and kinase-specific protein phosphorylation sites.

Proper citation: Musite (RRID:SCR_012141) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/automotifserver/

Software that predicts the wide selection of 88 different types of the single amino acid post-translational modifications (PTM) in protein sequences. The source code and precompiled binaries of brainstorming tool are available under Apache licensing.

Proper citation: AMS (RRID:SCR_012140) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/phosphosite/

A bioinformatical software tool for analyzing (quantitative) phosphoproteome datasets. The program retrieves kinase-substrate predictions from NetworKIN and contains various statistical modules for futher analysis.

Proper citation: PhosphoSiteAnalyzer (RRID:SCR_012142) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/hlaforest/

Software that predicts HLA haplotype by hierarchically weighting reads and using an iterative, greedy, top down pruning technique. HLAforest uses BioPerl to read in FASTA files. Alignments use Bow tie, although any alignment tool can be used to generate SAM alignments for use as input to HLAforest.

Proper citation: HLAforest (RRID:SCR_012146) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.12/bioc/html/DNAcopy.html

Software that segments DNA copy number data using circular binary segmentation to detect regions with abnormal copy number.

Proper citation: DNAcopy (RRID:SCR_012560) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/ExiMiR.html

R functions for the normalization of Exiqon miRNA array data.

Proper citation: ExiMiR (RRID:SCR_012753) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/cnv/

Software for a web-enabled platform for analyzing genome variation such as copy number variation (CNV).

Proper citation: CNV Workshop (RRID:SCR_012635) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/motifRG.html

Software tools for discriminative motif discovery using regression methods.

Proper citation: motifRG (RRID:SCR_012602) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/MiRaGE.html

Software package that contains functions for inference of target gene regulation by miRNA, based on only target gene expression profile.

Proper citation: MiRaGE (RRID:SCR_012738) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/CexoR.html

Software for strand specific peak-pair calling in ChIP-exo replicates.

Proper citation: CexoR (RRID:SCR_012769) Copy   

•   Source: SciCrunch Registry

http://tare.medisin.ntnu.no/motiflab/

Software for a general workbench for analyzing regulatory sequence regions and discovering transcription factor binding sites and cis-regulatory modules.

Proper citation: MotifLab (RRID:SCR_012649) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/tRanslatome.html

Detection of differentially expressed genes (DEGs) from the comparison of two biological conditions among different levels of gene expression, using several statistical methods: Rank Product, t-test, SAM, Limma, ANOTA, DESeq, edgeR.

Proper citation: tRanslatome (RRID:SCR_012810) Copy   

•   Source: SciCrunch Registry