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http://www.bioconductor.org/packages/2.13/bioc/html/cqn.html

A normalization tool for RNA-Seq data, implementing the conditional quantile normalization method.

Proper citation: CQN (RRID:SCR_001786) Copy   

•   Source: SciCrunch Registry

http://meme-suite.org/

Suite of motif-based sequence analysis tools to discover motifs using MEME, DREME (DNA only) or GLAM2 on groups of related DNA or protein sequences; search sequence databases with motifs using MAST, FIMO, MCAST or GLAM2SCAN; compare a motif to all motifs in a database of motifs; associate motifs with Gene Ontology terms via their putative target genes, and analyze motif enrichment using SpaMo or CentriMo. Source code, binaries and a web server are freely available for noncommercial use.

Proper citation: MEME Suite - Motif-based sequence analysis tools (RRID:SCR_001783) Copy   

•   Source: SciCrunch Registry

http://pfind.ict.ac.cn/se/plink/

Software dedicated for the analysis of chemically cross-linked proteins or protein complexes using mass spectrometry., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: pFind Studio: pLink (RRID:SCR_000084) Copy   

•   Source: SciCrunch Registry

http://www.psygenet.org/web/PsyGeNET/menu;jsessionid=y6kqy9lqlxymr0nwwkkfo84

Knowledge platform on psychiatric disorders and their genes. Resource for exploratory analysis of psychiatric diseases and their associated genes. PsyGeNET is composed of database and set of analysis tools and is the result of the integration of information from DisGeNET and data extracted from the literature by text mining, followed by curation by domain experts.

Proper citation: PsyGeNET (RRID:SCR_014406) Copy   

•   Source: SciCrunch Registry

http://scratch.proteomics.ics.uci.edu/index.html

Web protein structure and structural feature prediction server.Software suite includes predictors for secondary structure, relative solvent accessibility, disordered regions, domains, disulfide bridges, single mutation stability, residue contacts versus average, individual residue contacts and tertiary structure. User provides amino acid sequence and selects desired predictions, then submits to the server.

Proper citation: SCRATCH (RRID:SCR_014291) Copy   

•   Source: SciCrunch Registry

http://sysbio.rnet.missouri.edu/multicom_toolbox/NNCon%201.0.html

Protein contact map prediction is useful for protein folding rate prediction, model selection and 3D structure prediction. Here we describe NNcon, a fast and reliable contact map prediction server and software. NNcon was ranked among the most accurate residue contact predictors in the Eighth Critical Assessment of Techniques for Protein Structure Prediction (CASP8), 2008.

Proper citation: NNcon (RRID:SCR_014292) Copy   

•   Source: SciCrunch Registry

http://zhanglab.ccmb.med.umich.edu/I-TASSER/

Web server as integrated platform for automated protein structure and function prediction. Used for protein 3D structure prediction. Resource for automated protein structure prediction and structure-based function annotation.

Proper citation: I-TASSER (RRID:SCR_014627) Copy   

•   Source: SciCrunch Registry

http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/

Software tool for transcriptome assembly and differential expression analysis for RNA-Seq. Includes script called cuffmerge that can be used to merge together several Cufflinks assemblies. It also handles running Cuffcompare as well as automatically filtering a number of transfrags that are likely to be artifacts. If the researcher has a reference GTF file, the researcher can provide it to the script to more effectively merge novel isoforms and maximize overall assembly quality.

Proper citation: Cufflinks (RRID:SCR_014597) Copy   

•   Source: SciCrunch Registry

http://rast.nmpdr.org

A SEED-quality automated service that annotates complete or nearly complete bacterial and archaeal genomes across the entire phylogenetic tree. RAST can also be used to analyze draft genomes.

Proper citation: RAST Server (RRID:SCR_014606) Copy   

•   Source: SciCrunch Registry

http://bix.ucsd.edu/repeatscout/

Algorithm used to identify de novo repeat families in newly sequenced genomes. Repeat libraries for C. briggsae, M. muscles (X chromosome), R. novegicus (X chromosome), armadillo, H. sapiens (X chromosome), and various other mammals created using RepeatScout are available on the main site., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: RepeatScout (RRID:SCR_014653) Copy   

•   Source: SciCrunch Registry

http://www.vicbioinformatics.com/software.prokka.shtml

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on February 28,2023. Software tool for the rapid annotation of prokaryotic genomes. It produces GFF3, GBK and SQN files that are ready for editing in Sequin and ultimately submitted to Genbank/DDJB/ENA. A typical 4 Mbp genome can be fully annotated in less than 10 minutes on a quad-core computer, and scales well to 32 core SMP systems., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Prokka (RRID:SCR_014732) Copy   

•   Source: SciCrunch Registry

http://www.sailing.cs.cmu.edu/main/?page_id=511

Automatic software program for profiling spatial gene expression patterns from Fly embryo ISH images. It utilizes image-based genome-scale profiling of whole-body mRNA patterns.

Proper citation: SPEX2 (RRID:SCR_014923) Copy   

•   Source: SciCrunch Registry

https://dogma.ccbb.utexas.edu/

Web-based annotation tool for plant chloroplasts and animal mitochondrial genomes. DOGMA allows the use of BLAST searches against a custom database, and conservation of basepairing in the secondary structure of animal mitochondrial tRNAs to identify and annotate genes.

Proper citation: DOGMA (RRID:SCR_015060) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.psb.ugent.be/orcae/

Online genome annotation tool for validating and correcting gene annotations. OrcAE is community-driven and can be edited by account-holders in the research community.

Proper citation: Online Resource for Community Annotation of Eukaryotes (RRID:SCR_014989) Copy   

•   Source: SciCrunch Registry

http://www.mybiosoftware.com/seaview-4-2-12-sequence-alignment-phylogenetic-tree-building.html

Graphical user interface for multiple sequence alignment and molecular phylogeny. SeaView also generates phylogenetic trees.

Proper citation: SeaView (RRID:SCR_015059) Copy   

•   Source: SciCrunch Registry

http://www.stavroX.com

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on June 29,2023. Software tool for the analysis of cross-linking/mass spectrometry datasets using MS-cleavable cross-linkers. MeroX is specialized for MS/MS-cleavable cross linking reagents and identifies the specific fragmentation products of the cleavable cross links.

Proper citation: MeroX (RRID:SCR_014956) Copy   

•   Source: SciCrunch Registry

http://busco.ezlab.org/

Software tool to quantitatively measure genome assembly and annotation completeness based on evolutionarily informed expectations of gene content.

Proper citation: BUSCO (RRID:SCR_015008) Copy   

•   Source: SciCrunch Registry

http://paintmychromosomes.com/

Software tool as algorithm for identifying population structure using dense sequencing data. Can perform model based Bayesian clustering on large datasets, including full resequencing data.

Proper citation: fineSTRUCTURE (RRID:SCR_018170) Copy   

•   Source: SciCrunch Registry

https://github.com/yousra291987/ChiCMaxima

Pipeline for analyzing and identificantion of chromatin loops in CHi-C promoters data. Used to capture Hi-C visualization and interaction calling.

Proper citation: ChiCMaxima (RRID:SCR_018178) Copy   

•   Source: SciCrunch Registry

https://github.com/esctrionsit/snphub

Web Shiny-based server framework for retrieving, analyzing and visualizing large genomic variations data.

Proper citation: SnpHub (RRID:SCR_018177) Copy   

•   Source: SciCrunch Registry