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http://www.repeatmasker.org/RepeatModeler/
Sequence analysis software that performs repeat family identification and creates models for sequence data. RepeatModeler utilizes RepeatScout and RECON to identify repeat element boundaries and family relationships., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: RepeatModeler (RRID:SCR_015027) Copy
http://deweylab.biostat.wisc.edu/detonate/
Software tool to evaluate de novo transcriptome assemblies from RNA-Seq data. Consists of RSEM-EVAL and REF-EVAL packages. RSEM-EVAL is reference-free evaluation method. REF-EVAL is reference based and can be used to compare sets of any kinds of genomic sequences.
Proper citation: DETONATE (RRID:SCR_017035) Copy
Web app that allows users to search for the most important paths connecting any two nodes in Hetionet.
Proper citation: Hetnet Connectivity Search (RRID:SCR_023630) Copy
Open source relational database of signaling and metabolic molecules and their relations organized into biological pathways and processes. Core unit of Reactome data model is the reaction. Entities (nucleic acids, proteins, complexes, vaccines, anti-cancer therapeutics and small molecules) participating in reactions form network of biological interactions and are grouped into pathways including classical intermediary metabolism, signaling, transcriptional regulation, apoptosis and disease. External domain expert provides expertise, curator formalizes it into database structure, and external domain expert reviews representation. System of evidence tracking ensures that all assertions are backed up by primary literature. Website is designed to give the user graphical map of known biological processes and pathways that is also an interface. Database and website enable to find, organize, and utilize biological information to support data visualization, integration and analysis.
Proper citation: Reactome Knowledgebase (RRID:SCR_023504) Copy
https://imputationserver.sph.umich.edu/index.html#!pages/home
Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4.
Proper citation: Michigan Imputation Server (RRID:SCR_023554) Copy
Ratings or validation data are available for this resource
Human and mouse genome annotation project which aims to identify all gene features in the human genome using computational analysis, manual annotation, and experimental validation.
Proper citation: GENCODE (RRID:SCR_014966) Copy
https://github.com/fritzsedlazeck/Sniffles
Software tool as structural variation caller using third generation sequencing (PacBio or Oxford Nanopore). It detects all types of SVs (10bp+) using evidence from split-read alignments, high-mismatch regions, and coverage analysis. Used to avoid single molecule long read sequencing high error rates.
Proper citation: Sniffles (RRID:SCR_017619) Copy
https://genome.ucsc.edu/cgi-bin/hgLiftOver
Web tool to convert genome coordinates and genome annotation files between assemblies. Used to translate genomic coordinates from one assembly version into another and retrieves putative orthologous regions in other species using UCSC chained and netted alignments.
Proper citation: liftOver (RRID:SCR_018160) Copy
http://www.proteometools.org/index.php?id=home
Project for building molecular and digital tools from human proteome to facilitate biomedical research, drug discovery, personalized medicine and life science research.
Proper citation: ProteomeTools (RRID:SCR_018535) Copy
https://github.com/brentp/mosdepth
Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes.
Proper citation: mosdepth (RRID:SCR_018929) Copy
Web accessible database for visualizing and mining global yeast genetic interaction network. Allows users to easily access, visualize, explore, and functionally annotate genetic interactions, or to extract and reorganize sub networks, using data driven network layouts in intuitive and interactive manner. Used for storing and visualizing genetic interactions in S. cerevisiae.
Proper citation: TheCellMap (RRID:SCR_018728) Copy
Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature.
Proper citation: RegulomeDB (RRID:SCR_017905) Copy
https://data.broadinstitute.org/alkesgroup/Eagle/
Software package for statistical estimation of haplotype phase either within a genotyped cohort or using a phased reference panel in large scale sequencing. The package includes Eagle1 (to harness identity-by-descent among distant relatives to rapidly call phase using a fast scoring approach) and Eagle2 (to analyze a full probabilistic model similar to the diploid Li-Stephens model used by previous HMM-based methods.
Proper citation: Eagle (RRID:SCR_015991) Copy
Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated.
Proper citation: Mash (RRID:SCR_019135) Copy
http://llama.mshri.on.ca/funcassociate/
A web-based tool that accepts as input a list of genes, and returns a list of GO attributes that are over- (or under-) represented among the genes in the input list. Only those over- (or under-) representations that are statistically significant, after correcting for multiple hypotheses testing, are reported. Currently 37 organisms are supported. In addition to the input list of genes, users may specify a) whether this list should be regarded as ordered or unordered; b) the universe of genes to be considered by FuncAssociate; c) whether to report over-, or under-represented attributes, or both; and d) the p-value cutoff. A new version of FuncAssociate supports a wider range of naming schemes for input genes, and uses more frequently updated GO associations. However, some features of the original version, such as sorting by LOD or the option to see the gene-attribute table, are not yet implemented. Platform: Online tool
Proper citation: FuncAssociate: The Gene Set Functionator (RRID:SCR_005768) Copy
http://rulai.cshl.edu/cgi-bin/tools/ESE3/esefinder.cgi?process=home
A web-based resource that facilitates rapid analysis of exon sequences to identify putative exonic splicing enhancers (ESEs) responsive to the human SR proteins SF2/ASF, SC35, SRp40 and SRp55, and to predict whether exonic mutations disrupt such elements.
Proper citation: ESEfinder 3.0 (RRID:SCR_007088) Copy
http://ccr.coriell.org/Sections/Collections/NHGRI/?SsId=11
DNA samples and cell lines from fifteen populations, including the samples used for the International HapMap Project, the HapMap 3 Project and the 1000 Genomes Project (except for the CEPH samples). All of the samples were contributed with consent to broad data release and to their use in many future studies, including for extensive genotyping and sequencing, gene expression and proteomics studies, and all other types of genetic variation research. NHGRI led the contribution of the NIH to the International HapMap Project, which developed a haplotype map of the human genome. This haplotype map, called the HapMap is a publicly available tool that allows researchers to find genes and genetic variations that affect health and disease. The samples from four populations used to develop the HapMap were initially housed in the Human Genetic Cell Repository of the National Institute of General Medical Sciences (NIGMS). Except for the Utah CEPH samples that were in the NIGMS Repository before the initiation of the HapMap Project and remain there, the NHGRI Repository now houses all of the HapMap samples. The NHGRI repository also houses the extended set of HapMap samples, which includes additional samples from the HapMap populations and samples from seven additional populations. All of the samples were collected with extensive community engagement, including discussions with members of the donor communities about the ethical and social implications of human genetic variation research. These samples were studied as part of the HapMap 3 Project. The NHGRI repository also houses the samples for the International 1000 Genomes Project. This Project is lightly sequencing genome-wide 2500 samples from 27 populations. This project aims to provide a detailed map of human genetic variation, including common and rare SNPs and structural variants. This map will allow more precise localization of genomic regions that contribute to health and disease. The 1000 Genomes Project includes many of the samples from the HapMap and extended set of HapMap samples, as well as samples being collected from additional populations. Currently, samples from five additional populations are available; the others will become available during 2011 and 2012. No identifying or phenotypic information is available for the samples. Donors gave broad consent for use of the samples, including for genotyping, sequencing, and cellular phenotype studies. Samples collected from other populations for the study of human genetic variation may be added to the collection in the future. The NHGRI Repository distributes high quality lymphoblastoid cell lines and DNA from the samples to researchers. DNA is provided in plates or panels of 70 to 100 samples or as individual samples. Cell cultures and DNA samples are distributed only to qualified professional persons who are associated with recognized research, medical, educational, or industrial organizations engaged in health-related research or health delivery.
Proper citation: NHGRI Sample Repository for Human Genetic Research (RRID:SCR_004528) Copy
Software tool to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically. It counts cells and also measures the size, shape, intensity and texture of every cell (and every labeled subcellular compartment) in every image. It was designed for high throughput screening but can perform automated image analysis for images from time-lapse movies and low-throughput experiments. CellProfiler has an increasing number of algorithms to identify and measure properties of neuronal cell types.
Proper citation: CellProfiler Image Analysis Software (RRID:SCR_007358) Copy
https://jackbibby1.github.io/SCPA/
Software R package for pathway analysis in scRNA-seq data. It’s a different approach to pathway analysis that defines pathway activity as a change in multivariate distribution of a given pathway across conditions, rather than enrichment or over representation of genes.
Proper citation: Single Cell Pathway Analysis (RRID:SCR_024909) Copy
https://github.com/willtownes/glmpca
Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data.
Proper citation: glmpca (RRID:SCR_025517) Copy
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