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http://floresta.eead.csic.es/3dfootprint

Database of DNA-binding protein structures that is updated with Protein Data Bank complexes. It provides structure-based binding specificities and sequence logos, classification and clusters of protein-DNA interfaces, and downloads/stats.

Proper citation: 3D-footprint (RRID:SCR_015713) Copy   

•   Source: SciCrunch Registry

https://www.proteomicsdb.org/

Database for the identification of the human proteome and its use across the scientific community. Users can browse proteins and chromosomes and contribute to the data repository.

Proper citation: ProteomicsDB (RRID:SCR_015562) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/EGSEA/

Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets.

Proper citation: EGSEA (RRID:SCR_015036) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/datasets2tools/

Database for the discovery and evaluation of biomedical digital objects. It includes a wide variety of enrichment analyses, gene interaction networks, interactive data visualizations, datasets, and computational tools.

Proper citation: Datasets2Tools (RRID:SCR_016174) Copy   

•   Source: SciCrunch Registry

http://www.cuilab.cn/transmir

Collection of transcription factor microRNA regulations. TransmiR v2.0 manually curated TF-miRNA regulations from publications during 2013-2017 and included ChIP-seq-derived TF-miRNA regulation data.

Proper citation: TransmiR (RRID:SCR_017499) Copy   

•   Source: SciCrunch Registry

https://www.hmtvar.uniba.it

Manually curated database offering variability and pathogenicity information about mtDNA variants. Human mitochondrial variants data of healthy and diseased subjects.Data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information.

Proper citation: HmtVar (RRID:SCR_017288) Copy   

•   Source: SciCrunch Registry

http://bloodexposome.org

Collection of chemical compounds and associated information that were automatically extracted by text mining content of PubMed and PubChem databases. Unifies chemical lists from metabolomics, systems biology, environmental epidemiology, occupational expossure, toxiology and nutrition fields.

Proper citation: Blood Exposome Database (RRID:SCR_017610) Copy   

•   Source: SciCrunch Registry

http://apps.cytoscape.org/apps/pepper

A Cytoscape app designed to identify protein pathways / complexes as densely connected subnetworks from seed lists of proteins derived from pull-down assays (i.e AP-MS...).

Proper citation: PEPPER (RRID:SCR_000431) Copy   

•   Source: SciCrunch Registry

http://animalgene.umn.edu/locusmap/index.html

Software package designed for rapid linkage analysis and map construction of loci with a variety of inheritance modes. (entry from Genetic Analysis Software)

Proper citation: LOCUSMAP (RRID:SCR_000840) Copy   

•   Source: SciCrunch Registry

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

Software package that implements and enhances circular visualization in R. Due to natural born feature of R to draw statistical graphics, this package can provide more general and flexible way to visualize huge information in circular style.

Proper citation: circlize (RRID:SCR_002141) Copy   

•   Source: SciCrunch Registry

http://gusevlab.org/projects/germline/

Software application for discovering long shared segments of Identity by Descent (IBD) between pairs of individuals in a large population. It takes as input genotype or haplotype marker data for individuals (as well as an optional known pedigree) and generates a list of all pairwise segmental sharing., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: GERMLINE (RRID:SCR_001720) Copy   

•   Source: SciCrunch Registry

http://gmt.genome.wustl.edu/packages/breakdancer/

A Perl/C++ software package that provides genome-wide detection of structural variants from next generation paired-end sequencing reads. BreakDancerMax predicts five types of structural variants: insertions, deletions, inversions, inter- and intra-chromosomal translocations from next-generation short paired-end sequencing reads using read pairs that are mapped with unexpected separation distances or orientation. (entry from Genetic Analysis Software)

Proper citation: BREAKDANCER (RRID:SCR_001799) Copy   

•   Source: SciCrunch Registry

http://haplopainter.sourceforge.net/

A pedigree drawing program, suitable in processing haplotype outputs from GENEHUNTER, ALLEGRO, MERLIN, and SIMWALK (entry from Genetic Analysis Software)

Proper citation: HAPLOPAINTER (RRID:SCR_001710) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/CBBresearch/Schaffer/pedhunter.html

Software package that facilitates creation and verification of pedigrees within large genealogies. The pedigrees are produced as files in LINKAGE format ready for linkage analysis and for drawing with a variety of drawing programs, such as PEDDRAW and cranefoot.

Proper citation: PEDHUNTER (RRID:SCR_002031) Copy   

•   Source: SciCrunch Registry

http://ngsutils.org/

A suite of software tools for analyzing and manipulating next-generation sequencing datasets, such as FASTQ, BED and BAM format files. These tools provide a stable and modular platform for data management and analysis.

Proper citation: NGSUtils (RRID:SCR_001236) Copy   

•   Source: SciCrunch Registry

http://people.virginia.edu/~wc9c/TDTPC/Download.htm

Software program to compute the statistical power of the Transmission/Disequilibrium Test (TDT) analytically, based on the most accurate asymptotic algorithms up to date, and is applicable in very general situations, where different parental disease status, multiple children, mixed family type and recombination events are considered. Routine algorithms for Monte Carlo simulations with significant improvements are also implemented in this program. (entry from Genetic Analysis Software)

Proper citation: TDT-PC (RRID:SCR_001116) Copy   

•   Source: SciCrunch Registry

http://khmer.readthedocs.org/

Software library and suite of command line tools for working with DNA sequence that takes a k-mer-centric approach to sequence analysis. It is primarily aimed at short-read sequencing data such as that produced by the Illumina platform.

Proper citation: khmer (RRID:SCR_001156) Copy   

•   Source: SciCrunch Registry

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

Software R package to model and impute non-detects in results of qPCR experiments.Used to directly model non-detects as missing data.

Proper citation: nondetects (RRID:SCR_001702) Copy   

•   Source: SciCrunch Registry

http://clip.med.yale.edu/presto/

Software toolkit for processing raw reads from high-throughput sequencing of lymphocyte repertoires.

Proper citation: pRESTO (RRID:SCR_001782) Copy   

•   Source: SciCrunch Registry

http://subread.sourceforge.net/

Software package for high-performance read alignment, quantification and mutation discovery.General purpose read aligner which can be used to map both genomic DNA-seq reads and RNA-seq reads. Subread aligner as fast, accurate and scalable read mapping by seed-and-vote.These programs were also implemented in Bioconductor R package Rsubread.

Proper citation: Subread (RRID:SCR_009803) Copy   

•   Source: SciCrunch Registry