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https://github.com/bsml320/Scupa/

Software R package for immune cell polarization assessment of scRNA-seq data. Single-cell unified polarization assessment of immune cells using single-cell foundation model. Used for comprehensive immune cell polarization analysis.

Proper citation: Scupa (RRID:SCR_025755) Copy   

•   Source: SciCrunch Registry

https://microbiomap.org

Microbial ecology dataset describing the composition of publicly available human microbiome samples deposited in INSDC databases (Sequence Read Archive, European Nucleotide Archive, Digital Data Bank of Japan). Genus-level read counts are available for more than 168,000 samples from around the world, with additional curated metadata for samples and projects.

Proper citation: Human Microbiome Compendium (RRID:SCR_026991) Copy   

•   Source: SciCrunch Registry

https://github.com/McGranahanLab/TcellExTRECT

Software R package to calculate T cell fractions from WES data from hg19 or hg38 aligned genomes.

Proper citation: T Cell ExTRECT (RRID:SCR_027742) Copy   

•   Source: SciCrunch Registry

https://github.com/bsml320/NetBCE

Software tool used to predict linear B-cell epitopes (BCEs) from protein sequences. It helps scientists find parts of a pathogen that trigger immune responses. Interpretable deep neural network for accurate prediction of linear B-cell epitopes.

Proper citation: NetBCE (RRID:SCR_028677) Copy   

•   Source: SciCrunch Registry

http://www.coremine.com/medical/#search

Service to access comprehensive information on diseases, drugs, treatments and medical biology. It is ideal for those seeking an overview of a complex subject while allowing the possibility to drill down to specific details. Search results are presented in a dashboard format comprized of panels containing various categories of information ranging from introductory sources to the latest scientific articles.

Proper citation: Coremine Medical (RRID:SCR_005323) Copy   

•   Source: SciCrunch Registry

http://amp.pharm.mssm.edu/X2K/

Software tool to produce inferred networks of transcription factors, proteins, and kinases predicted to regulate the expression of the inputted gene list by combining transcription factor enrichment analysis, protein-protein interaction network expansion, with kinase enrichment analysis. It provides the results as tables and interactive vector graphic figures.

Proper citation: eXpression2Kinases (RRID:SCR_016307) Copy   

•   Source: SciCrunch Registry

https://github.com/slowkoni/rfmix

Software tool for local ancestry and admixture inference. Discriminative Modeling Approach for Rapid and Robust Local-Ancestry Inference.

Proper citation: RFMix (RRID:SCR_027030) Copy   

•   Source: SciCrunch Registry

https://github.com/epistasislab/hibachi

Software tool that creates data sets with particular characteristics. Method and open source software for simulating complex biological and biomedical data to aid in comparing and evaluating machine learning methods.

Proper citation: Heuristic Identification of Biological Architectures for simulating Complex Hierarchical Interactions (RRID:SCR_017140) Copy   

•   Source: SciCrunch Registry

http://ailun.stanford.edu/

Re-annotated gene expression / proteomics data from GEO by relating all probe IDs to Entrez Gene IDs once every three months, enabling you to find data from GEO, and compare them from different platforms and species. Platform Annotations adds the latest annotations to any uploaded probe / gene ID list file. Platform Comparison compares any two platforms to find corresponding probes mapping to the same gene. Cross-species mapping maps platform annotations to other species. Gene Search finds deposited platforms and samples in GEO that contain a list of genes. GPL ID Search finds the GPL ID (GEO platform ID) for your array. You can also download the latest annotations files for all arrays and their comprehensive universal gene identifier table, which relates all types of gene / protein / clone identifiers to Entrez Gene IDs for all species. Note: The database was last updated on 4/30/2011. They have successfully mapped 54932732 individual probes from 385099 GEO samples measuring 3519 GEO platforms across 217 species.

Proper citation: Array Information Library Universal Navigator (RRID:SCR_006967) Copy   

•   Source: SciCrunch Registry

http://virtualhumanembryo.lsuhsc.edu/

A digital image database of serially sectioned human embryos from the Carnegie Collection originally developed as a collaboration between embryologist Dr. Raymond Gasser at Louisiana State University Health Science Center (LSUHSC) and the Human Developmental Anatomy Center (HDAC) in Washington D.C. The aim of the project is to increase understanding of human embryology and to encourage study of human embryonic development by providing students and researchers with reliable resources for human embryo morphology. The VHE project has several components: * DREM: The Digitally Reproduced Embryonic Morphology (DREM) project, with funding from NICHD, project has produced 27 image databases of labeled serial sections from representative human embryos at each of the 23 Carnegie stages. These databases, together with animations and reconstructions of the embryos are available on DVD and CD. * HEIRLOOM: The HEIRLOOM Collection (Human Embryo Imaging and Reconstruction, Library Of Online Media) was funded by the National Library of Medicine to provide greater access to the DREM databases. NLM provided funding to set up this website and to produce additional 3D-reconstructions and animations that are included on the DREM disks. Original website, http://virtualhumanembryo.lsuhsc.edu/HEIRLOOM/heirloom.htm * EHD: Starting in 2011, The Endowment for Human Development (EHD) will also host the VHE databases. They have made the project accessible to everyone and include a comprehensive cataloging of all the terms used to label the embryos. Their website enables users to browse through the complete VHE atlas of human embryology, http://www.ehd.org/virtual-human-embryo/

Proper citation: Virtual Human Embryo (RRID:SCR_006921) Copy   

•   Source: SciCrunch Registry

http://senselab.med.yale.edu/ordb/

Database of vertebrate olfactory receptors genes and proteins. It supports sequencing and analysis of these receptors by providing a comprehensive archive with search tools for this expanding family. The database also incorporates a broad range of chemosensory genes and proteins, including the taste papilla receptors (TPRs), vomeronasal organ receptors (VNRs), insect olfaction receptors (IORs), Caenorhabditis elegans chemosensory receptors (CeCRs), and fungal pheromone receptors (FPRs). ORDB currently houses chemosensory receptors for more than 50 organisms. ORDB contains public and private sections which provide tools for investigators to analyze the functions of these very large gene families of G protein-coupled receptors. It also provides links to a local cluster of databases of related information in SenseLab, and to other relevant databases worldwide. The database aims to house all of the known olfactory receptor and chemoreceptor sequences in both nucleotide and amino acid form and serves four main purposes: * It is a repository of olfactory receptor sequences. * It provides tools for sequence analysis. * It supports similarity searches (screens) which reduces duplicate work. * It provides links to other types of receptor information, e.g. 3D models. The database is accessible to two classes of users: * General public www users have full access to all the public sequences, models and resources in the database. * Source laboratories are the laboratories that clone olfactory receptors and submit sequences in the private or public database. They can search any sequence they deposited to the database against any private or public sequence in the database. This user level is suited for laboratories that are actively cloning olfactory receptors.

Proper citation: Olfactory Receptor DataBase (RRID:SCR_007830) Copy   

•   Source: SciCrunch Registry

http://rebase.neb.com/rebase/

Database of information about restriction enzymes and related proteins containing published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal, genome, and sequence data. DNA methyltransferases, homing endonucleases, nicking enzymes, specificity subunits and control proteins are also included. Several tools are available including REBsites, BLAST against REBASE, NEBcutter and REBpredictor. Putative DNA methyltransferases and restriction enzymes, as predicted from analysis of genomic sequences, are also listed. REBASE is updated daily and is constantly expanding. Users may submit new enzyme and/or sequence information, recommend references, or send them corrections to existing data. The contents of REBASE may be browsed from the web and selected compilations can be downloaded by ftp (ftp.neb.com). Additionally, monthly updates can be requested via email.,

Proper citation: REBASE (RRID:SCR_007886) Copy   

•   Source: SciCrunch Registry

https://github.com/YuanXue1993/SegAN

Image analysis software for medical image segmentation. The software is fueled by an end-to-end adversarial neural network that generates segmentation label maps.

Proper citation: SegAN (RRID:SCR_016215) Copy   

•   Source: SciCrunch Registry

http://hanalyzer.sourceforge.net/

An open-source data integration system designed to assist biologists in explaining the results observed in genome-scale experiments as well as generating new hypotheses. It combines information extraction techniques, semantic data integration, and reasoning and facilitates network visualization. The Hanalyzer source code and binaries are available for download.

Proper citation: Hanalyzer (RRID:SCR_000923) Copy   

•   Source: SciCrunch Registry

http://toxnet.nlm.nih.gov/cgi-bin/sis/htmlgen?DARTETIC

Bibliographic database providing references to developmental and reproductive toxicology literature on the National Library of Medicine's Toxicology Data Network. It covers teratology and other aspects of developmental and reproductive toxicology. It contains over 200,000 references to literature published since 1965. DART/ETIC is easily accessible and free of charge. Search by subject terms, title words, chemical name, Chemical Abstracts Service Registry Number (RN), and author. Search results can easily be viewed, printed or downloaded. Search results are displayed in relevancy ranked order, but may be sorted by publication date, author or title.

Proper citation: Developmental and Reproductive Toxicology Database (RRID:SCR_002326) Copy   

•   Source: SciCrunch Registry

http://www.clairlib.org

A suite of open-source Perl modules intended to simplify a number of generic tasks in natural language processing (NLP), information retrieval (IR), and network analysis (NA). Its architecture also allows for external software to be plugged in with very little effort. The latest version of clairlib is 1.06 which was released on March 2009 and includes about 130 modules implementing a wide range of functionalities. Clairlib is distributed in two forms: * Clairlib-core, which has essential functionality and minimal dependence on external software, and * Clairlib-ext, which has extended functionality that may be of interest to a smaller audience. Much can be done using Clairlib on its own. Some of the things that Clairlib can do are: Tokenization, Summarization, Document Clustering, Document Indexing, Web Graph Analysis, Network Generation, Power Law Distribution Analysis, Network Analysis, RandomWalks on Graphs, Tf-IDF, Perceptron Learning and Classification, and Phrase Based Retrieval and Fuzzy OR Queries.

Proper citation: Clair library (RRID:SCR_007019) Copy   

•   Source: SciCrunch Registry

http://www.ncbi.nlm.nih.gov/pubmedcommons/

A forum where authors who have published in PubMed may comment on any publication in PubMed. Members of PubMed Commons are not anonymous and must agree to certain terms and guidelines concerning appropriate and inapproriate comments.

Proper citation: Pubmed Commons (RRID:SCR_014021) Copy   

•   Source: SciCrunch Registry

https://integrativeomics.shinyapps.io/pseudofun_app/

Software as database and query tool for homologous pseudogene and coding gene families. Collection of human pseudogenes and gene associations. Supports search, graphical visualization and functional analysis of pseudogenes and coding genes based on PGG families.

Proper citation: PseudoFuN (RRID:SCR_017095) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://vanvalen.github.io/about/

Software for segmenting individual cells in microscopy images using deep learning. Cell segmentation software.

Proper citation: DeepCell (RRID:SCR_022197) Copy   

•   Source: SciCrunch Registry