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http://www.scbi.uma.es/ingebiol/session/new/seqtrimnext

A customizable and distributed pre-processing software for NGS (Next Generation Sequencing) biological data.The old version for Sanger sequences, Seqtrim, has been discontinued.

Proper citation: SeqtrimNEXT (RRID:SCR_011845) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/~zerbino/oases/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool as de novo transcriptome assembler designed to produce transcripts from short read sequencing technologies, such as Illumina, SOLiD, or 454 in the absence of any genomic assembly.

Proper citation: Oases (RRID:SCR_011896) Copy   

•   Source: SciCrunch Registry

http://tophat.cbcb.umd.edu/fusion_index.html

An algorithm for Discovery of Novel Fusion Transcripts with the ability to align reads across fusion points, which results from the breakage and re-joining of two different chromosomes, or from rearrangements within a chromosome.

Proper citation: TopHat-Fusion (RRID:SCR_011899) Copy   

•   Source: SciCrunch Registry

http://genome.ucsc.edu/cgi-bin/hgBlat?command=start

Software designed to quickly find sequences of 95% and greater similarity of length 25 bases or more.

Proper citation: BLAT (RRID:SCR_011919) Copy   

•   Source: SciCrunch Registry

http://www.bios.unc.edu/research/genomic_software/BBSeq/

A Powerful and Flexible Approach to the Analysis of RNA Sequence Count Data.

Proper citation: BBSeq (RRID:SCR_011877) Copy   

•   Source: SciCrunch Registry

http://i.cs.hku.hk/~alse/hkubrg/projects/idba_ud/

Software for an iterative De Bruijn Graph De Novo Assembler for Short Reads Sequencing data with Highly Uneven Sequencing Depth.

Proper citation: IDBA-UD (RRID:SCR_011912) Copy   

•   Source: SciCrunch Registry

http://www.unav.es/genetica/oncofuse.html

Software tool designed to predict the oncogenic potential of fusion genes found by Next-Generation Sequencing in cancer cells.

Proper citation: Oncofuse (RRID:SCR_011904) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.mdanderson.org/main/PRADA:Overview

A pipeline to analyze paired end RNA-Seq data to generate gene expression values (RPKM) and gene-fusion candidates.

Proper citation: PRADA (RRID:SCR_011906) Copy   

•   Source: SciCrunch Registry

https://mcdonaldlab.biology.gatech.edu/r-sap/

An automated bioinformatics pipeline that analyzes and quantitates high-throughput RNA-Seq datasets.

Proper citation: R-SAP (RRID:SCR_011907) Copy   

•   Source: SciCrunch Registry

http://mapman.gabipd.org/web/guest/robin

Software package for RNA-Seq-based transcriptomics. Used to analyse Illumina/Solexa-based RNA-Seq data, Affymetrix data and generic tabular two color or single channel array data. Offers variety of quality control methods that can be used to gain overview of experimental data technical quality and structure.

Proper citation: RobiNA (RRID:SCR_011908) Copy   

•   Source: SciCrunch Registry

http://www.optimaldesign.com/ArrayMiner/ArrayMiner.htm

A set of analysis tools using advanced algorithms to reveal the true structure of your gene expression data.

Proper citation: ArrayMiner (RRID:SCR_011955) Copy   

•   Source: SciCrunch Registry

https://www.sanger.ac.uk/science/tools/caf

Software tools for manipulating Common Assembly Format files text format for describing sequence assemblies,that can be downloaded from the Sanger ftp site.

Proper citation: caftools (RRID:SCR_023982) Copy   

•   Source: SciCrunch Registry

http://ingenium.home.xs4all.nl/dicom.html

Software for DICOM training and testing,Demonstration and research image archives,Image format conversion from scanner with DICOM network access,DICOM image viewing and slide making, DICOM image selection, (limited) editing, and splitting and merging of series, Advanced scriptable image modification, filtering, forwarding and conversion, DICOM caching and archive merging, DICOM web access for viewing and data management (scriptable),Connection to Lua IDE for all sorts of DICOM manipulation.

Proper citation: Conquest DICOM (RRID:SCR_023993) Copy   

•   Source: SciCrunch Registry

https://github.com/pennsignals/chime

Software designed to assist hospitals and public health officials with understanding hospital capacity needs as they relate to the COVID pandemic. CHIME enables capacity planning by providing estimates of total daily and running totals of inpatient hospitalizations, ICU admissions, and patients requiring ventilation.

Proper citation: CHIME (RRID:SCR_023987) Copy   

•   Source: SciCrunch Registry

https://genome.sph.umich.edu/wiki/EMMAX

Software statistical test for large scale human or model organism association mapping accounting for the sample structure. In addition to the computational efficiency obtained by EMMA algorithm, EMMAX takes advantage of the fact that each loci explains only a small fraction of complex traits, which allows us to avoid repetitive variance component estimation procedure, resulting in a significant amount of increase in computational time of association mapping using mixed model.

Proper citation: EMMAX (RRID:SCR_024012) Copy   

•   Source: SciCrunch Registry

http://www.dicompyler.com/

Software extensible open source radiation therapy research platform based on the DICOM standard. It also functions as a cross-platform DICOM RT viewer.

Proper citation: dicompyler (RRID:SCR_024006) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/foreign/index.html

Software tool for reading and writing data stored by some versions of 'Epi Info', 'Minitab', 'S', 'SAS', 'SPSS', 'Stata', 'Systat', 'Weka', and for reading and writing some 'dBase' files.

Proper citation: foreign (RRID:SCR_024025) Copy   

•   Source: SciCrunch Registry

https://github.com/rrwick/Deepbinner

Software tool for demultiplexing barcoded Oxford Nanopore sequencing reads.Signal level demultiplexer for Oxford Nanopore reads.

Proper citation: Deepbinner (RRID:SCR_024001) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://crac.gforge.inria.fr/

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   

•   Source: SciCrunch Registry