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https://weghornlab.org/software.html
Software tool which derives gene-specific probabilistic estimates of the strength of negative and positive selection in cancer.
Proper citation: CBaSE (RRID:SCR_027765) Copy
https://github.com/vanallenlab/comut
Software Python library for creating comutation plots to visualize genomic and phenotypic information. Used for visualizing genomic and phenotypic information via comutation plots.
Proper citation: CoMUT (RRID:SCR_027745) Copy
https://github.com/SalasLab/HiTIMED
Software DNA methylation-based algorithm, to estimate cell proportions in tumor microenvironment. Profiles tumor, immune, and angiogenic components, allowing researchers to study tumor composition and its clinical implications using archival biospecimens.
Proper citation: HiTIMED (RRID:SCR_028180) Copy
Database offers integrated multi-omic data for patients across 33 cancer types. It encompasses gene expression, DNA methylation, somatic mutations, proteomic profiles, and chromatin accessibility, drawing from TCGA, GTEx, and CPTAC projects. Users can compare gene expression, DNA methylation, and protein levels between tumor and normal tissues, identifying differentially expressed genes and proteins, and examining gene-to-gene correlations. Provides oncogene mutation profiles and allows for survival analysis based on gene expression and methylation, linked to clinical parameters. Facilitates exploration of multi-omic correlations, such as gene expression with DNA methylation, and their variations with mutation status. Extends its analytical capabilities to include six major oncoviruses, offering insights into their impact on gene expression, methylation, and patient survival.
Proper citation: OncoDB (RRID:SCR_028340) Copy
http://www.dbmi.pitt.edu/nlpfront
THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 17, 2013. Repository of de-identified clinical reports available for NLP researchers has been designed. Work with the AMIA NLP working group in designing annotation schemas and obtaining annotations, design a repository for shareable annotations, help design and execute a shared task in IE from clinical reports. The University of Pittsburgh NLP Repository contains clinical reports that are available to the community for NLP research purposes and comprises: # Report Repository - one month of de-identified clinical reports from multiple hospitals and # Annotation Repository - annotations performed on reports from the Report Repository. Anyone performing annotations on reports from the NLP Repository is required to deposit their annotations. The Repository contains reports of the following types generated from multiple hospitals during a single month: * History and Physicals * Progress Notes * Consultation Reports * Radiology Reports * Surgical Pathology Reports * Emergency Department Reports * Discharge Summaries * Operative Reports * Cardiology Reports
Proper citation: Open Clinical Report Repository (RRID:SCR_013585) Copy
http://wiki.c2b2.columbia.edu/honiglab_public/index.php/Software:Jackal
Jackal is a collection of programs designed for the modeling and analysis of protein structures. Its core program is a versatile homology modeling package. It contains twelve individual programs, each with their own function.
Proper citation: Jackal (RRID:SCR_008665) Copy
https://www.nature.com/articles/s41467-018-03367-w
Nanodroplet processing platform for deep and quantitative proteome profiling of 10 to 100 mammalian cells. It enhances efficiency and recovery of sample processing by downscaling processing volumes.
Proper citation: nanoPOTS (RRID:SCR_017129) Copy
http://compgen.bscb.cornell.edu/phast/
A freely available software package for comparative and evolutionary genomics that consists of about half a dozen major programs, plus more than a dozen utilities for manipulating sequence alignments, phylogenetic trees, and genomic annotations. For the most part, PHAST focuses on two kinds of applications: the identification of novel functional elements, including protein-coding exons and evolutionarily conserved sequences; and statistical phylogenetic modeling, including estimation of model parameters, detection of signatures of selection, and reconstruction of ancestral sequences. It consists of over 60,000 lines of C code.
Proper citation: PHAST (RRID:SCR_003204) Copy
http://rankprop.gs.washington.edu/svm-fold/
This web server makes predictions of family, superfamily and fold level classifications of proteins based on the Structural Classification of Proteins (SCOP) hierarchy using the Support Vector Machine (SVM) learning algorithm. SVM-FOLD detects subtle protein sequence similarities by learning from all available annotated proteins, as well as utilizing potential hits as identified by PSI-BLAST. Predictions of classes of proteins that do not have any known example with a significant pairwise PSI-BLAST E-value can still be found using SVMs.
Proper citation: SVM-fold: Protein Fold Prediction (RRID:SCR_006834) Copy
Service to discover disease genes in GWAS using eQTL signature matching by simply submitting your list of GWAS associations (SNPs and p-values). It is important to upload all SNPs in your association study, not just the top hits. Sherlock may be able to group multiple lower-confidence SNPs to discover functionally-important genes.
Proper citation: Sherlock (RRID:SCR_001628) Copy
https://github.com/SciKnowEngine/kefed.io
Knowledge engineering software for reasoning with scientific observations and interpretations. The software has three parts: (a) the KEfED model editor - a design editor for creating KEfED models by drawing a flow diagram of an experimental protocol; (b) the KEfED data interface - a spreadsheet-like tool that permits users to enter experimental data pertaining to a specific model; (c) a "neural connection matrix" interface that presents neural connectivity as a table of ordinal connection strengths representing the interpretations of tract-tracing data. This tool also allows the user to view experimental evidence pertaining to a specific connection. The KEfED model is designed to provide a lightweight representation for scientific knowledge that is (a) generalizable, (b) a suitable target for text-mining approaches, (c) relatively semantically simple, and (d) is based on the way that scientist plan experiments and should therefore be intuitively understandable to non-computational bench scientists. The basic idea of the KEfED model is that scientific observations tend to have a common design: there is a significant difference between measurements of some dependent variable under conditions specified by two (or more) values of some independent variable.
Proper citation: Knowledge Engineering from Experimental Design (RRID:SCR_001238) Copy
http://publications.nigms.nih.gov/insidelifescience/
The NIGMS Inside Life Science series brings you inside the science of health. Each story shows how basic biomedical researchfrom the history of a field to the people doing cutting-edge work todaylays the foundation for advances in disease diagnosis, treatment and prevention. Through explorations of how the body works and highlights from recent studies, you''ll discover even more on what scientists have found and are finding about fundamental life processes. NIGMS supported all of the featured research.
Proper citation: NIGMS Inside Life Science (RRID:SCR_005852) Copy
Collection of revertible protein trap gene-breaking transposon (GBT) insertional mutants in zebrafish with active or cryopreserved lines from initially identified lines. Open to community-wide contributions including expression and functional annotation and represents world-wide central hub for information on how to obtain these lines from diverse members of International Zebrafish Protein Trap Consortium (IZPTC) and integration within other zebrafish community databases including Zebrafish Information Network (ZFIN), Ensembl and National Center for Biotechnology Information. Registration allows users to save their favorite lines for easy access, request lines from Mayo Clinic catalog, contribute to line annotation with appropriate credit, and puts them on optional mailing list for future zfishbook newletters and updates.
Proper citation: zfishbook (RRID:SCR_006896) Copy
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
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3149502/
Software for comprehensive quantitative measure of splicing impact of complete set of RNA 6-mer sequences by deep sequencing successfully spliced transcripts.
Proper citation: ESRseq score (RRID:SCR_022270) Copy
Software for statistical approach to identify loci within genes that are both significantly enriched in slowly translated codons and evolutionarily conserved, and also co-translational protein folding model.
Proper citation: Coarse grained co-translational folding analysis (RRID:SCR_022271) Copy
http://www.sci.utah.edu/cibc/software/231-biomesh3d.html
A free, easy to use program for generating quality meshes for use in biological simulations. It is currently integrated with SCIRun and uses the SCIRun system to visualize the intermediate results. The BioMesh3D program uses a particle system to distribute nodes on the separating surfaces that separate the different materials and then uses the TetGen software package to generate a full tetrahedral mesh.
Proper citation: BioMesh3D (RRID:SCR_009534) Copy
Software tool to detect differential alternative splicing events from RNA-Seq data. Calculates P-value and false discovery rate that difference in isoform ratio of gene between two conditions exceeds given user-defined threshold. From RNA-Seq data can automatically detect and analyze alternative splicing events corresponding to all major types of alternative splicing patterns. Handles replicate RNA-Seq data from both paired and unpaired study design.
Proper citation: rMATS (RRID:SCR_023485) Copy
https://bioxtas-raw.readthedocs.io/en/latest/
Software tool as GUI based Python program for reduction and analysis of small-angle X-ray solution scattering (SAXS) data.Small-angle scattering data reduction and analysis. Available on Windows, macOS (and OS X), and Linux.
Proper citation: BioXTAS RAW (RRID:SCR_025769) Copy
A freely accessible on-line systems biology resource devoted to all aspects of protein modification, as well as other post-translational modifications. It provides valuable and unique tools for both cell biologists and mass spectroscopists. PhosphoSite is a human- and mouse-centric database. It includes features such as: viewing the locations of modified residues on molecular models; browsing and searching MS2 records by disease, tissue, and cell line; submitting lists of peptides to identify previously reported genes; searching by sub-cellular localization, treatment, tissues, cell types, cell lines and diseases, and protein types and protein domains; searching for experimentally-verified kinase substrates and viewing preferred substrate motifs; and viewing MS2 spectra for peptides and sites not previously published.
Proper citation: PhosphoSitePlus: Protein Modification Site (RRID:SCR_001837) Copy
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