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http://dna.engr.uconn.edu/?page_id=105
Software package that can be used to infer isoform and gene expression levels from high-throughput transcriptome sequencing (RNA-Seq) data.
Proper citation: IsoEM (RRID:SCR_009993) Copy
http://code.google.com/p/bitseq/
A software application for inferring expression levels of individual transcripts from sequencing (RNA-Seq) data and estimating differential expression (DE) between conditions.
Proper citation: BitSeq (RRID:SCR_009904) Copy
http://www.genome.umd.edu/masurca.html
A whole genome assembly software that combines the efficiency of the de Bruijn graph and Overlap-Layout-Consensus (OLC) approaches., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MaSuRCA (RRID:SCR_010691) Copy
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Integrated RNA-Seq read analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CRAC (RRID:SCR_010652) Copy
https://confluence.crbs.ucsd.edu/display/NIF/OntoQuestMain
An ontology management module to perform ontology-based search over data sources. This management system permits a user to store, search and navigate any number of OWL-structured ontologies. Ontoquest may also be accessed through a variety of web services via the Neuroscience Information Framework.
Proper citation: OntoQuest (RRID:SCR_013281) Copy
http://rdxplorer.sourceforge.net/
A computational tool for copy number variants (CNV) detection in whole human genome sequence data using read depth (RD) coverage.
Proper citation: RDXplorer (RRID:SCR_013290) Copy
http://alumni.cs.ucr.edu/~liw/cem.html
An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.
Proper citation: CEM (RRID:SCR_013241) Copy
Software for a normalization scheme that corrects nucleotide composition bias, mappability variations and differential local DNA structural effects in deep sequencing data.
Proper citation: BEADS (RRID:SCR_013229) Copy
http://www.bcgsc.ca/platform/bioinfo/software/trans-abyss
A software pipeline for analyzing ABySS-assembled contigs from shotgun transcriptome data.
Proper citation: Trans-ABySS (RRID:SCR_013322) Copy
http://code.google.com/p/chimerascan/
Software package that detects gene fusions in paired-end RNA sequencing (RNA-Seq) datasets. Used for detection of chimeric transcripts in high-throughput sequencing data.
Proper citation: chimerascan (RRID:SCR_013298) Copy
http://bioinfo.au.tsinghua.edu.cn/software/pcs/
A stand-alone package to identify and analyze conserved k-mers in pairwise alignment. This program shows high performance for identifying miRNA seed binding sites in 3''-UTRs.
Proper citation: Pairwise Conservation Scores - An Algorithm to Identify Conserved K-mers (RRID:SCR_013409) Copy
http://www.eisenlab.org/eisen/?page_id=42
Software to graphically browse results of clustering and other analyses from Cluster.
Proper citation: TreeView (RRID:SCR_013503) Copy
http://tiger.dbs.nus.edu.sg/cnv-seq/
A method for detecting DNA copy number variation (CNV) using high-throughput sequencing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: CNV-seq (RRID:SCR_013357) Copy
http://amp.pharm.mssm.edu/clustergrammer/
Clustergrammer is a web-based tool for visualizing and analyzing high-dimensional data as interactive and shareable hierarchically clustered heatmaps. Clustergrammer enables intuitive exploration of high-dimensional data and has several optional biology-specific features.
Proper citation: clustergrammer (RRID:SCR_015681) Copy
https://sites.google.com/a/lbl.gov/biopig/
Software providing a framework for genomic data analysis using Apache Pig and Hadoop.
Proper citation: BioPig (RRID:SCR_004636) Copy
http://bioinformatics.rutgers.edu/Software/SLiQ/
Software for simple linear inequalities based Mate-Pair reads filtering and scaffolding. A set of simple linear inequalities (SLIQ) derived from the geometry of contigs on the line that can be used to predict the relative positions and orientations of contigs from individual mate pair reads and thus produce a contig digraph. The SLIQ inequalities can also filter out unreliable mate pairs and can be used as a pre-processing step for any scaffolding algorithm. This tool filters mate pairs and then produces a Directed Contig Graph (contig diGraph). Also provided is a Naive scaffolder that can then produce scaffolds out of the contig diGraph.
Proper citation: SLIQ (RRID:SCR_005003) Copy
http://www.physics.rutgers.edu/~anirvans/SOPRA/
Software tool to exploit the mate pair/paired-end information for assembly of short reads from high throughput sequencing platforms, e.g. Illumina and SOLiD.
Proper citation: SOPRA (RRID:SCR_005035) Copy
http://www.baseclear.com/landingpages/basetools-a-wide-range-of-bioinformatics-solutions/sspacev12/
A stand-alone software program for scaffolding pre-assembled contigs using paired-read data. Main features are: a short runtime, multiple library input of paired-end and/or mate pair datasets and possible contig extension with unmapped sequence reads.
Proper citation: SSPACE (RRID:SCR_005056) Copy
http://cran.r-project.org/web/packages/MBCluster.Seq/index.html
Software to cluster genes based on Poisson or Negative-Binomial model for RNA-Seq or other digital gene expression (DGE) data.
Proper citation: MBCluster.Seq (RRID:SCR_005079) Copy
https://github.com/AlexeyG/GRASS
A generic algorithm for scaffolding next-generation sequencing assemblies.
Proper citation: GRASS (RRID:SCR_005071) Copy
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