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

A Java interface to the mzTab data exchange format for reporting a summary of proteomics results.

Proper citation: jmzTab (RRID:SCR_003481) Copy   

•   Source: SciCrunch Registry

http://www.compgen.org/tools/metagen

Software program providing a method for meta-analysis of case-control genetic association studies using random-effects logistic regression.

Proper citation: metagen (RRID:SCR_003443) Copy   

•   Source: SciCrunch Registry

http://genome.sph.umich.edu/wiki/RAREMETAL

A software program that facilitates the meta-analysis of rare variants from genotype arrays or sequencing.

Proper citation: RAREMETAL (RRID:SCR_003573) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/2.11/bioc/html/ShortRead.html

Software package for input, quality assessment and exploration of high-throughput sequence data. Used for input, quality assurance, and basic manipulation of `short read'' DNA sequences such as those produced by Solexa, 454, and related technologies, including exible import of common short read data formats.

Proper citation: ShortRead (RRID:SCR_006813) Copy   

•   Source: SciCrunch Registry

https://github.com/friend1ws/EBCall

A software package for somatic mutation detection (including InDels). EBCall uses not only paired tumor/normal sequence data of a target sample, but also multiple non-paired normal reference samples for evaluating distribution of sequencing errors, which leads to an accurate mutaiton detection even in case of low sequencing depths and low allele frequencies.

Proper citation: EBCall (RRID:SCR_006791) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/2.9/bioc/html/RamiGO.html

Software package with an R interface sending requests to AmiGO visualize, retrieving DAG GO trees, parsing GraphViz DOT format files and exporting GML files for Cytoscape. Also uses RCytoscape to interactively display AmiGO trees in Cytoscape.

Proper citation: RamiGO (RRID:SCR_006922) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/artfastqgen/

Software to evaluate and improve the accuracy of sequencing error under different experimental conditions. It can identify which components of a system may be suboptimal and which regions of the genome may be problematic.

Proper citation: ArtificialFastqGenerator (RRID:SCR_006880) Copy   

•   Source: SciCrunch Registry

http://seqbarracuda.sourceforge.net/

A sequence mapping software that utilizes the massive parallelism of graphics processing units to accelerate the inexact alignment of short sequence reads to a particular location on a reference genome. It can align a paired-end library containing 14 million pairs of 76bp reads to the Human genome in about 27 minutes (from fastq files to SAM alignment) using a ��380 NVIDIA Geforce GTX 680*. The alignment throughput can be boosted further by using multiple GPUs (up to 8) at the same time. Being based on BWA (http://bio-bwa.sf.net) from the Sanger Institute, BarraCUDA delivers a high level of alignment fidelity and is comparable to other mainstream alignment programs. It can perform gapped alignment with gap extensions, in order to minimise the number of false variant calls in re-sequencing studies.

Proper citation: BarraCUDA (RRID:SCR_006881) Copy   

•   Source: SciCrunch Registry

http://bowtie-bio.sourceforge.net/myrna/index.shtml

A cloud computing tool for calculating differential gene expression in large RNA-seq datasets. It uses Bowtie for short read alignment and R/Bioconductor for interval calculations, normalization, and statistical testing. These tools are combined in an automatic, parallel pipeline that runs in the cloud (Elastic MapReduce in this case) on a local Hadoop cluster, or on a single computer, exploiting multiple computers and CPUs wherever possible.

Proper citation: Myrna (RRID:SCR_006951) Copy   

•   Source: SciCrunch Registry

http://bioinfo3d.cs.tau.ac.il/FlexProt/

FlexProt detects the optimal flexible structural alignment of a pair of protein structures. The first structure is assumed to be rigid, while in the second structure potential flexible regions are automatically detected.

Proper citation: FlexProt: flexible protein alignment (RRID:SCR_007306) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/taipan/

A fast hybrid short-read assembly tool.

Proper citation: Taipan (RRID:SCR_007330) Copy   

•   Source: SciCrunch Registry

http://www.stat.brown.edu/ZWU/research.aspx

Borrows information across sequences to establish prior distribution of sample variation, so that biological variation can be accounted for even when replicates are not available.

Proper citation: ASC (RRID:SCR_001013) Copy   

•   Source: SciCrunch Registry

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

A Java application programming interface (API) for the Proteomics Standards Initiative mzML data standard.

Proper citation: jmzML (RRID:SCR_001119) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/devel/bioc/html/massiR.html

Software that predicts the sex of samples in gene expression microarray datasets.

Proper citation: massiR (RRID:SCR_001157) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/~stijn/reaper/reaper.html

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23, 2022. Software program for demultiplexing, trimming and filtering short read sequencing data.

Proper citation: Reaper - Demultiplexing trimming and filtering sequencing data (RRID:SCR_001144) Copy   

•   Source: SciCrunch Registry

https://rdrr.io/bioc/yaqcaffy/

Software package for quality control of Affymetrix GeneChip expression data and reproducibility analysis of human whole genome chips with the MAQC reference datasets.

Proper citation: yaqcaffy (RRID:SCR_001295) Copy   

•   Source: SciCrunch Registry

http://montgomerylab.stanford.edu/spliceplot/index.html

A software tool for visualizing alternative splicing and the effects of splicing quantitative trait loci (sQTLs) from RNA-seq data. It provides a simple command line interface for drawing sashimi plots, hive plots, and structure plots of alternative splicing events from .bam, .gtf, and .vcf files.

Proper citation: SplicePlot (RRID:SCR_001172) Copy   

•   Source: SciCrunch Registry

http://julian-gehring.github.io/les/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software package that estimates Loci of Enhanced Significance (LES) in tiling microarray data. These are regions of regulation such as found in differential transcription, CHiP-chip, or DNA modification analysis. The package provides a universal framework suitable for identifying differential effects in tiling microarray data sets, and is independent of the underlying statistics at the level of single probes.

Proper citation: les (RRID:SCR_001291) Copy   

•   Source: SciCrunch Registry

http://qualimap.bioinfo.cipf.es/

Software application written in Java and R that provides both a Graphical User Inteface (GUI) and a command-line interface to facilitate the quality control of alignment sequencing data. It examines sequencing alignment data in SAM / BAM files according to the features of the mapped reads and provides an overall view of the data that helps to the detect biases in the sequencing and/or mapping of the data and eases decision-making for further analysis.

Proper citation: QualiMap (RRID:SCR_001209) Copy   

•   Source: SciCrunch Registry

http://pathology.wustl.edu/VirusHunter/

A fully automated and modular software package for mining sequence data to identify sequences of microbial origin. The pipeline was optimized for analysis of data generated by the Roche/454 next-generation sequencing platform but can be applied to longer sequences (Sanger sequencing data or assembled contigs) as well. Microbial sequences are identified on the basis of BLAST alignments and the taxonomic classification of the reference sequence(s) to which a read is aligned. Viruses are the focal point of VirusHunter as released, but it can be easily modified to generate parallel outputs for bacterial or parasitic species. To date, VirusHunter has been applied to thousands of specimens, including human, animal and environmental samples, resulting in the detection of many known and novel viruses.

Proper citation: VirusHunter (RRID:SCR_001198) Copy   

•   Source: SciCrunch Registry