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https://github.com/iontorrent/TMAP
Alignment software for short and long nucleotide sequences produced by next-generation sequencing technologies.
Proper citation: TMAP (RRID:SCR_000687) Copy
https://code.google.com/p/glycoworkbench/
A suite of software tools designed for the rapid drawing of glycan structures and for assisting the process of structure determination from mass spectrometry data.
Proper citation: GlycoWorkbench (RRID:SCR_000782) Copy
http://www.brown.edu/Research/Istrail_Lab/hapcompass.php
Software that utilizes a fast cycle basis algorithm for the accurate haplotype assembly of sequence data. It is able to create pairwise SNP phasings.
Proper citation: HapCompass (RRID:SCR_000942) Copy
https://github.com/akiomiyao/tif
A search program to detect insertions of transposable element from short reads of next generation sequencer.
Proper citation: Transposon Insertion Finder (RRID:SCR_001159) Copy
http://www.bioconductor.org/packages/2.13/bioc/html/bsseq.html
R package with tools for analyzing and visualizing bisulfite sequencing data.
Proper citation: bsseq (RRID:SCR_001072) Copy
http://www.bioconductor.org/packages/release/bioc/html/MmPalateMiRNA.html
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 23,2022. Software R package written for analysis of murine palate miRNA two-color expression data.
Proper citation: MmPalateMiRNA (RRID:SCR_001070) Copy
http://www.bioconductor.org/packages/2.10/bioc/html/R453Plus1Toolbox.html
R software toolbox of functions for the analysis of data generated by Roche's 454 sequencing platform. Additional functions are included for quality assurance, annotation and visualization of detected variants, complementing the software tools shipped by Roche with their product. A pipeline for the detection of structural variants is provided.
Proper citation: R453Plus1Toolbox (RRID:SCR_001105) Copy
http://www.bioconductor.org/packages/release/bioc/html/RmiR.html
R package that contains functions to merge microRNA and respective targets using different databases.
Proper citation: RmiR (RRID:SCR_001069) Copy
http://bioinformatics.mdanderson.org/main/BreakFusion
Software package written in Perl and C++ that provides a computational pipeline for identifying gene fusions from RNA-seq data.
Proper citation: BreakFusion (RRID:SCR_001102) Copy
https://omictools.com/npebseq-tool
A method for non-parametric, empirical Bayesian-based analysis of RNA-seq count data.
Proper citation: NPEBseq (RRID:SCR_001014) Copy
https://omictools.com/splitseek-tool
THIS RESOURCE IS NO LONGER IN SERVICE, documented September 20, 2016. A program for de novo prediction of splice junctions in RNA-seq data.
Proper citation: SplitSeek (RRID:SCR_001012) Copy
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
http://www.bioconductor.org/packages/2.12/bioc/html/jmosaics.html
R software that detects enriched regions of ChIP-seq data sets jointly.
Proper citation: Jmosaics (RRID:SCR_001094) Copy
A C++ application designed for compression of genome collections from the same species.
Proper citation: GDC (RRID:SCR_001007) Copy
http://sourceforge.net/projects/autoassemblyd/
Software which performs local and remote genome assembly by several assemblers based on an XML Template which can replace the large command lines required by most assemblers.
Proper citation: AutoAssemblyD (RRID:SCR_001087) Copy
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
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
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
http://www.codoncode.com/productsservices/phrap.htm#PHRED
A base calling program for DNA sequence traces.
Proper citation: Phred (RRID:SCR_001017) Copy
A tool for creating logos representing both sequence alignments and profile hidden Markov models. The interactive logos enable scrolling, zooming, and inspection of underlying values. Skylign can avoid sampling bias in sequence alignments by down-weighting redundant sequences and by combining observed counts with informed priors. It also simplifies the representation of gap parameters, and can optionally scale letter heights based on alternate calculations of the conservation of a position.
Proper citation: Skylign (RRID:SCR_001176) Copy
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