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https://earray.chem.agilent.com/cghanalytics/index.html

A comprehensive design and analysis tool for setting up and interpreting your microarray experiments.

Proper citation: Agilent Genomic Workbench (RRID:SCR_010918) Copy   

•   Source: SciCrunch Registry

http://pages.cs.wisc.edu/~kliang/DBChIP/

Detects differential binding of transcription factors with ChIP-seq.

Proper citation: DBChIP (RRID:SCR_010872) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/DIME/index.html

R-package for identifying differential ChIP-seq based on an ensemble of mixture models.

Proper citation: DIME (RRID:SCR_010874) Copy   

•   Source: SciCrunch Registry

http://www.cs.ucf.edu/~xiaoman/ChIPModule/ChIPModule.html

A software tool for systematic discovery of transcription factors and their cofactors from ChIP-seq data.

Proper citation: ChIPModule (RRID:SCR_010877) Copy   

•   Source: SciCrunch Registry

http://bio-bwa.sourceforge.net/

Software for aligning sequencing reads against large reference genome. Consists of three algorithms: BWA-backtrack, BWA-SW and BWA-MEM. First for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.

Proper citation: BWA (RRID:SCR_010910) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/apps/mediawiki/cloudburst-bio/index.php?title=CloudBurst

A new parallel read-mapping algorithm optimized for mapping next-generation sequence data to the human genome and other reference genomes, for use in a variety of biological analyses including SNP discovery, genotyping, and personal genomics.

Proper citation: CloudBurst (RRID:SCR_010911) Copy   

•   Source: SciCrunch Registry

http://erne.sourceforge.net/

A short string alignment package whose goal is to provide an all-inclusive set of tools to handle short (NGS-like) reads.

Proper citation: ERNE (RRID:SCR_010912) Copy   

•   Source: SciCrunch Registry

http://fureylab.web.unc.edu/software/fseq/

A software package that generates a continuous tag sequence density estimation allowing identification of biologically meaningful sites whose output can be displayed directly in the UCSC Genome Browser.

Proper citation: F-Seq (RRID:SCR_010880) Copy   

•   Source: SciCrunch Registry

http://homer.ucsd.edu/

Software tools for Motif Discovery and next-gen sequencing analysis. Used for analyzing ChIP-Seq, GRO-Seq, RNA-Seq, DNase-Seq, Hi-C and numerous other types of functional genomics sequencing data sets. Collection of command line programs for unix style operating systems written in Perl and C++.

Proper citation: HOMER (RRID:SCR_010881) Copy   

•   Source: SciCrunch Registry

http://megasun.bch.umontreal.ca/People/lartillot/www/

A Bayesian Monte Carlo Markov Chain (MCMC) sampler software for phylogenetic reconstruction. Its main distinguishing feature is the underlying probabilistic model, CAT (Lartillot and Philippe, 2004). CAT is an infinite mixture model accounting for site-specific amino-acid or nucleotide preferences. It is well suited to phylogenomic studies using large multigene alignments., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: PhyloBayes (RRID:SCR_006402) Copy   

•   Source: SciCrunch Registry

http://kobas.cbi.pku.edu.cn/

Web server to identify statistically enriched pathways, diseases, and GO terms for a set of genes or proteins, using pathway, disease, and GO knowledge from multiple famous databases. It allows for both ID mapping and cross-species sequence similarity mapping. It then performs statistical tests to identify statistically significantly enriched pathways and diseases. KOBAS 2.0 incorporates knowledge across 1327 species from 5 pathway databases (KEGG PATHWAY, PID, BioCyc, Reactome and Panther) and 5 human disease databases (OMIM, KEGG DISEASE, FunDO, GAD and NHGRI GWAS Catalog). A standalone command line version is also available, THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: KOBAS (RRID:SCR_006350) Copy   

•   Source: SciCrunch Registry

http://snps.ccbr.utoronto.ca:8080/SNPdryad/

Service to predict deleterious non-synonymous human Single Nucleotide Polymorphisms (SNPs) using only orthologous protein sequences.

Proper citation: SNPdryad (RRID:SCR_006414) Copy   

•   Source: SciCrunch Registry

http://cran.r-project.org/web/packages/QCGWAS/

Software tools for (automated and manual) quality control of the results of Genome Wide Association Studies.

Proper citation: QCGWAS (RRID:SCR_006408) Copy   

•   Source: SciCrunch Registry

http://loschmidt.chemi.muni.cz/predictsnp/

Consensus classifier tool that combines six of the top performing tools for the prediction of the effects of mutation on protein function. The obtained results are provided together with annotations extracted from the Protein Mutant Database and the UniProt database. A stand-alone version is also available.

Proper citation: PredictSNP (RRID:SCR_006327) Copy   

•   Source: SciCrunch Registry

http://omim.org

Online catalog of human genes and genetic disorders, for clinical features, phenotypes and genes. Collection of human genes and genetic phenotypes, focusing on relationship between phenotype and genotype. Referenced overviews in OMIM contain information on all known mendelian disorders and variety of related genes. It is updated daily, and entries contain copious links to other genetics resources.

Proper citation: OMIM (RRID:SCR_006437) 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://bioinf.comav.upv.es/seq_crumbs/

A collection of small sequence processing utilities that are modeled after the Unix command line text processing utilities so every utility tries to perform a specific task and most of them take a sequence file as input and create a new processed sequence file as output. This design encourages the assembly of the seq_crumbs utilities with Unix pipes to create complex pipelines.

Proper citation: seq crumbs (RRID:SCR_006486) Copy   

•   Source: SciCrunch Registry

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

A software package for the discovery of regulatory regions from Bis-seq data.

Proper citation: MethylSeekR (RRID:SCR_006513) Copy   

•   Source: SciCrunch Registry

http://www.LOVD.nl/

Freely available tool for Gene-centered collection and display of DNA variations. It also provides patient-centered data storage and storage of Next Generation Sequencing (NGS) data, even of variants outside of genes. Please note that LOVD provides a system for storage of information on genes and allelic variants. To obtain information about any genes or variants, do not download the LOVD package. This information should be obtained from the respective databases, http://www.lovd.nl/2.0/index_list.php In total: 2,507,027 variants (2,208,937 unique) in 170,935 individuals in 62619 genes in 88 LOVD installations. (Aug. 2013) LOVD 3.0 shared installation, http://databases.lovd.nl/shared/genes To maintain a high quality of the data stored, LOVD connects with various resources, like HGNC, NCBI, EBI and Mutalyzer. You can download LOVD in ZIP and GZIPped TARball formats.

Proper citation: Leiden Open Variation Database (RRID:SCR_006566) Copy   

•   Source: SciCrunch Registry