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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://beads.sourceforge.net/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://www.jalview.org/

A free program for multiple sequence alignment editing, visualisation and analysis that is available in two forms: a lightweight Java applet for use in web applications, and a powerful desktop application that employs web services for sequence alignment, secondary structure prediction and the retrieval of alignments, sequences, annotation and structures from public databases and any DAS 1.53 compliant sequence or annotation server. Use it to view and edit sequence alignments, analyse them with phylogenetic trees and principal components analysis (PCA) plots and explore molecular structures and annotation. Jalview has built in DNA, RNA and protein sequence and structure visualisation and analysis capabilities. It uses Jmol to view 3D structures, and VARNA to display RNA secondary structure.

Proper citation: Jalview (RRID:SCR_006459) Copy   

•   Source: SciCrunch Registry

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

Software package to make access to the compilation of metadata from NCBI SRA and tools associated with submission, study, sample, experiment and run much more feasible. This is accomplished by parsing all the NCBI SRA metadata into a SQLite database that can be stored and queried locally. Fulltext search in the package make querying metadata very flexible and powerful. fastq and sra files can be downloaded for doing alignment locally. Beside ftp protocol, the SRAdb has funcitons supporting fastp protocol (ascp from Aspera Connect) for faster downloading large data files over long distance. The SQLite database is updated regularly as new data is added to SRA and can be downloaded at will for the most up-to-date metadata.

Proper citation: SRAdb (RRID:SCR_006524) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov

A portal to biomedical and genomic information. NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information for the better understanding of molecular processes affecting human health and disease.

Proper citation: NCBI (RRID:SCR_006472) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/release/bioc/html/casper.html

Software to infer alternative splicing from paired-end RNA-seq data. The model is based on counting paths across exons, rather than pairwise exon connections, and estimates the fragment size and start distributions non-parametrically, which improves estimation precision.

Proper citation: casper (RRID:SCR_006613) Copy   

•   Source: SciCrunch Registry

http://rulai.cshl.edu/splicetrap/

A statistic tool for quantifying exon inclusion ratios in paired-end RNA-seq data, with broad applications for the study of alternative splicing. SpliceTrap approaches to exon inclusion level estimation as a Bayesian inference problem. For every exon it quantifies the extent to which it is included, skipped or subjected to size variations due to alternative 3?/5? splice sites or Intron Retention. In addition, SpliceTrap can quantify alternative splicing within a single cellular condition, with no need of a background set of reads.

Proper citation: SpliceTrap (RRID:SCR_006728) Copy   

•   Source: SciCrunch Registry

https://github.com/arq5x/bedtools2

A powerful toolset for genome arithmetic allowing one to address common genomics tasks such as finding feature overlaps and computing coverage. Bedtools allows one to intersect, merge, count, complement, and shuffle genomic intervals from multiple files in widely-used genomic file formats such as BAM, BED, GFF/GTF, VCF. While each individual tool is designed to do a relatively simple task (e.g., intersect two interval files), quite sophisticated analyses can be conducted by combining multiple bedtools operations on the UNIX command line.

Proper citation: BEDTools (RRID:SCR_006646) Copy   

•   Source: SciCrunch Registry

http://www.broadinstitute.org/igv/

A high-performance visualization tool for interactive exploration of large, integrated genomic datasets.

Proper citation: Integrative Genomics Viewer (RRID:SCR_011793) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/tools/gbench/

An integrated application for viewing and analyzing sequence data.

Proper citation: NCBI Genome Workbench (RRID:SCR_011794) Copy   

•   Source: SciCrunch Registry

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

A software program that allows you to easily visualize your next-generation sequencing (NGS) samples at functional genomic regions.

Proper citation: ngs.plot (RRID:SCR_011795) Copy   

•   Source: SciCrunch Registry

http://www.cs.utah.edu/~miriah/mizbee/Overview.html

A multiscale synteny browser for exploring conservation relationships in comparative genomics data.

Proper citation: MizBee (RRID:SCR_011804) Copy   

•   Source: SciCrunch Registry

http://code.google.com/p/condetri/

Software tool as content dependent read trimmer for Illumina data. Content dependent read trimming software for Illumina/Solexa sequencing data.

Proper citation: ConDeTri (RRID:SCR_011838) Copy   

•   Source: SciCrunch Registry

http://circos.ca/

A software package for visualizing data and information. It visualizes data in a circular layout - this makes Circos ideal for exploring relationships between objects or positions.

Proper citation: Circos (RRID:SCR_011798) Copy   

•   Source: SciCrunch Registry