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https://ihg.helmholtz-muenchen.de/cgi-bin/hw/hwa1.pl

Software tool for performing tests for deviation from Hardy-Weinberg equilibrium and tests for association. Used in population-based genetic association studies to identify susceptibility genes for complex diseases.

Proper citation: Tests for deviation from Hardy-Weinberg equilibrium (RRID:SCR_016496) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/DGB/

Web based application to assist researchers with identifying drugs and small molecules that are predicted to maximally influence expression of mammalian gene of interest. Used to identify drugs and small molecules to regulate expression of target genes for research purpose only. Application for ranking drugs to modulate specific gene based on transcriptomic signatures.

Proper citation: Drug Gene Budger (RRID:SCR_016489) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/00-0210

Scanner for microarray analysis to scan next-generation higher-density arrays, including SNP arrays, tiling arrays for transcription and all-exon arrays for whole-genome analysis.

Proper citation: Thermo Fisher: GeneChip� Scanner 3000 7G (RRID:SCR_016522) Copy   

•   Source: SciCrunch Registry

https://www.ncbi.nlm.nih.gov/projects/gap/cgi-bin/study.cgi?study_id=phs000363.v16.p10

Project to generate extensive biomarker data from Framingham Heart Study participants using immunoassays, proteomics, metabolomics/lipomics, and gene expression and microRNA profiling to advance personalized medicine through biomarker discovery and validation.

Proper citation: SABRe CVD Initiative (RRID:SCR_016572) Copy   

•   Source: SciCrunch Registry

https://github.com/WGS-TB/MentaLiST

Software for a MLST (multi-locus sequence typing) caller, based on a k-mer counting algorithm and written in the Julia language. Designed and implemented to handle large typing schemes.

Proper citation: MentaLiST (RRID:SCR_016469) Copy   

•   Source: SciCrunch Registry

https://github.com/umerijaz/nanopore

Software for a workflow for amplicon sequencing from mixed microbial communities on the nanopore sequencing platform. Used for full-length SSU rRNA gene sequencing.

Proper citation: NanoAmpli-Seq (RRID:SCR_016710) Copy   

•   Source: SciCrunch Registry

https://github.com/iychoi/libra

Hadoop based tool for massive comparative metagenomics analysis. Compute the similarity between metagenomic samples.

Proper citation: Libra (RRID:SCR_016608) Copy   

•   Source: SciCrunch Registry

https://niaid.github.io/dcas/

Web tool to import raw cDNA sequences, clean sequences, build sequence contigs, perform SignalP analysis, BLAST contigs against numerous BLAST databases, and view the results. Automates large scale cDNA sequence analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: dCAS (RRID:SCR_016612) Copy   

•   Source: SciCrunch Registry

http://www.epilepsygenetics.eu/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on August 16,2023. Group of clinical care and epilepsy research centers who are committed to improving the lives of people with epilepsy through an understanding of the genetics of epilepsy. The consoritum was in an effort to speed discovery to epilepsy genetics by pooling the resources of several research centres., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: EPIGEN (RRID:SCR_000093) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/minet/

Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data.

Proper citation: minet (RRID:SCR_018661) Copy   

•   Source: SciCrunch Registry

https://mygene.info/

Web service for querying or retrieving gene annotation data.

Proper citation: MyGene.info (RRID:SCR_018660) Copy   

•   Source: SciCrunch Registry

http://rats.pub

Web service that conducts comprehensive literature mining to identify roles of genes in addiction. Searches PubMed to find abstracts containing genes of interest and list of curated addiction related keywords.

Proper citation: RatsPub (RRID:SCR_018905) Copy   

•   Source: SciCrunch Registry

http://tools.dice-database.org/GOnet/)

Web tool for interactive Gene Ontology analysis of any biological data sources resulting in gene or protein lists.

Proper citation: GOnet (RRID:SCR_018977) Copy   

•   Source: SciCrunch Registry

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

Software R package for statistical analysis and visualization of functional profiles for genes and gene clusters.

Proper citation: clusterProfiler (RRID:SCR_016884) Copy   

•   Source: SciCrunch Registry

https://picrust.github.io/picrust/

Software package to predict metagenome functional content from marker gene (e.g., 16S rRNA) surveys and full genomes. Used to predict which gene families are present and then combines gene families to estimate the composite metagenome.

Proper citation: PICRUSt (RRID:SCR_016855) Copy   

•   Source: SciCrunch Registry

https://www.stemformatics.org/#

Gene expression data portal developed for stem cell community, containing public gene expression datasets derived from microarray, RNA sequencing and single cell profiling technologies. Portal to visualize and download curated stem cell data. Provides easy to use and intuitive tools for biologists to visually explore data, including interactive gene expression profiles, principal component analysis plots and hierarchical clusters, among others.

Proper citation: Stemformatics (RRID:SCR_017002) Copy   

•   Source: SciCrunch Registry

https://github.com/lucapinello/Haystack

Software suite of computational tools implemented in Python to study epigenetic variability, cross cell type plasticity of chromatin states and transcription factors motifs providing mechanistic insights into chromatin structure, cellular identity and gene regulation. Epigenetic variability and transcription factor motifs analysis pipeline.

Proper citation: Haystack (RRID:SCR_017087) Copy   

•   Source: SciCrunch Registry

https://github.com/im3sanger/dndscv

Software R package as suite of dN/dS methods to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole genome level. Used to detect cancer driver genes on datasets.

Proper citation: dndSCV (RRID:SCR_017093) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/gage/

Software R package for gene set enrichment or pathway analysis. Applicable independent of microarray or RNAseq data attributes including sample sizes, experimental designs, assay platforms, and other types of heterogeneity. Pipeline routines of multiple GAGE analyses in batch, comparison between parallel analyses, and combined analysis of heterogeneous data from different sources and studies.

Proper citation: GAGE (RRID:SCR_017067) Copy   

•   Source: SciCrunch Registry

http://www.cbs.dtu.dk/services/RNAmmer/

Software package to predict ribosomal RNA genes in full genome sequences by utilising two levels of Hidden Markov Models. Consistent and rapid annotation of ribosomal RNA genes.

Proper citation: RNAmmer (RRID:SCR_017075) Copy   

•   Source: SciCrunch Registry