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https://combine-lab.github.io/salmon/
Software tool for quantifying expression of transcripts using RNA-seq data. Provides fast and bias-aware quantification of transcript expression. Transcriptome-wide quantifier to correct for fragment GC-content bias.
Proper citation: Salmon (RRID:SCR_017036) Copy
https://github.com/fmaguire/Bridger_Assembler
Software package as de novo trascriptome assembler for RNA-Seq data. Framework for de novo transcriptome assembly using RNA-seq data. Can assemble all transcripts from short reads without using reference. Input RNA-Seq reads in fasta or fastq format, and ouput all assembled candidate transcripts in fasta format. Operating system Unix/Linux.
Proper citation: Bridger (RRID:SCR_017039) Copy
https://pcago.bioinf.uni-jena.de/
Interactive web service for analysis of RNA-Seq read count data with principal component analysis (PCA) and agglomerative clustering. Includes features like read count normalization, filtering read counts by gene annotation and visualization options.
Proper citation: PCAGO (RRID:SCR_017033) Copy
https://github.com/jefferis/nat
Software R package for 3D visualisation and analysis of biological image data, especially tracings of single neurons.
Proper citation: NeuroAnatomy Toolbox (RRID:SCR_017248) Copy
https://bibiserv.cebitec.uni-bielefeld.de/pkiss
Software tool for folding RNA secondary structures, including two limited classes of pseudoknots. Performs abstract shape analysis for structures holding pseudoknots up to complexity of kissing hairpin motifs. Successor of pknotsRG. Used for secondary structure prediction including kissing hairpin motifs.
Proper citation: pKiss (RRID:SCR_017256) Copy
https://github.com/Barski-lab/cwl-airflow
Software Python package to extend Airflow functionality with Common Workflow Language support. Lightweight pipeline manager supporting Common Workflow Language. Can be used to run workflows on standalone MacOS/Linux servers, on clusters, or on cloud platforms.
Proper citation: CWL-Airflow (RRID:SCR_017196) Copy
https://www.beckman.it/flow-cytometry/research-flow-cytometers/cytoflex/software
Software program that controls instrument operation, data collection and analysis. Software for CytoFLEX Platform by Beckman Coulter.
Proper citation: CytExpert Software (RRID:SCR_017217) Copy
Software as set of commandline tools with GUI frontend that performs data reconstruction and fiber tracking on diffusion MR images. It does preparation work for TrackVis. Software Package for diffusion imaging data processing and tractography.
Proper citation: Diffusion Toolkit (RRID:SCR_017345) Copy
http://pathwaynet.princeton.edu/
Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.
Proper citation: PathwayNet (RRID:SCR_017353) Copy
https://github.com/ndierckx/NOVOPlasty
Software package as de novo assembler and heteroplasmy variance caller for short circular genomes. Used for de novo assembly of organelle genomes from whole genome data.
Proper citation: NOVOPlasty (RRID:SCR_017335) Copy
Software tool for automated removal of spurious sequences or poorly aligned regions from multiple sequence alignment. Software package for automated alignment trimming in large scale phylogenetic analyses.
Proper citation: trimAl (RRID:SCR_017334) Copy
https://github.com/YosefLab/FastProject
Software Python tool for low dimensional analysis of single-cell RNA-Seq data. Software package for two dimensional visualization of single cell data. Analyzes gene expression matrix and produces output report in which two-dimensional of data can be explored.
Proper citation: FastProject (RRID:SCR_017462) Copy
http://chemrich.fiehnlab.ucdavis.edu/
Software tool for chemical similarity enrichment analysis of metabolomics datasets. Used in studies to uncover biological mechanisms in organisms under genetic or environmental stress in system biology manner or finding risk factors for chronic diseases in exposome wise association studies using blood specimens. Allows users to realize pathway analysis.
Proper citation: ChemRICH (RRID:SCR_017609) Copy
http://easyfig.sourceforge.net/
A Python application for creating linear comparison figures of multiple genomic loci with an easy-to-use graphical user interface (GUI).
Proper citation: Easyfig (RRID:SCR_013169) Copy
http://microbiomeutil.sourceforge.net/#A_CS
A chimeric sequence detection utility, compatible with near-full length Sanger sequences and shorter 454-FLX sequences (~500 bp).
Proper citation: ChimeraSlayer (RRID:SCR_013283) Copy
http://sourceforge.net/projects/telescoper/
An algorithm that iteratively extends long paths through a series of read-overlap graphs and evaluates them based on a statistical framework.
Proper citation: Telescoper (RRID:SCR_013206) Copy
http://csbl.bmb.uga.edu/dbCAN/
A web server and DataBase for automated Carbohydrate-active enzyme ANnotation, funded by the BioEnergy Science Center of the DOE., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: dbCAN (RRID:SCR_013208) Copy
http://sourceforge.net/projects/palfinder/
A perl script that finds microsatellite repeat elements directly from raw 454 or Illumina paired-end sequencing reads.
Proper citation: palfinder (RRID:SCR_013174) Copy
http://alumni.cs.ucr.edu/~liw/isolasso.html
An algorithm to assemble transcripts and estimate their expression levels from RNA-Seq reads.
Proper citation: IsoLasso (RRID:SCR_013176) Copy
http://sourceforge.net/projects/samcomp/
A simple arithmetic coding based compressor for the SAM and BAM (DNA sequence alignment) file format.
Proper citation: sam comp (RRID:SCR_013179) Copy
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