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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://oncodb.org/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://sherlock.ucsf.edu/

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://zfishbook.org/

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   

•   Source: SciCrunch Registry

https://rmats.sourceforge.io

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   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/saint-apms/files/

Software tool for upgraded implementation of probabilistic scoring of affinity purification mass spectrometry data. Used for filtering high confidence interaction data from affinity purification mass spectrometry experiments. Used for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.

Proper citation: SAINTexpress (RRID:SCR_018562) Copy   

•   Source: SciCrunch Registry

https://psbweb05.psb.ugent.be/conet/microbialnetworks/spieceasi.php

Software R package estimates inverse covariance matrix from sequencing data.Statistical method for inference of microbial ecological networks from amplicon sequencing datasets.

Proper citation: Sparse Inverse Covariance Estimation for Ecological Association Inference (RRID:SCR_022646) Copy   

•   Source: SciCrunch Registry

https://cran.r-project.org/web/packages/BGLR/

Software R package implements large collection of Bayesian regression models, including parametric variable selection and shrinkage methods and semiparametric procedures.

Proper citation: Bayesian Generalized Linear Regression (RRID:SCR_022522) Copy   

•   Source: SciCrunch Registry

http://www.cgl.ucsf.edu/

Biomedical technology resource center that develops software and web-based resources for the visualization and analysis of molecular structure, and related data, at scales ranging from the atomic to the supramolecular. They create tools for handling and integrating diverse types of biomolecular data, including atomic-resolution coordinates, density maps, sequences, annotations, and networks. Their primary efforts are in the visualization and analysis of structures of molecules and molecular assemblies, enzyme sequence-structure-function relationships, and network representations of protein similarity, binding interactions, and biological pathways. They provide technologies to enable identifying the molecular bases of disease and phenotypic variation, annotating proteins of unknown function, identifying targets for drug development, designing drugs, and engineering proteins with new functions. RBVI distributes software tools, including the popular UCSF Chimera visualization and analysis package, develops and hosts the Structure-Function Linkage Database, and provides access to state-of-the-art computational resources in support of research projects in these areas.

Proper citation: Resource for Biocomputing Visualization and Informatics (RRID:SCR_001374) Copy   

•   Source: SciCrunch Registry

https://github.com/rondolab/MR-PRESSO

Software R package for performing Mendelian randomization pleiotropy residual sum and outlier method.Used to identify horizontal pleiotropic outliers in multi instrument summary level MR testing.

Proper citation: MR-PRESSO (RRID:SCR_023697) Copy   

•   Source: SciCrunch Registry

http://anya.igsb.anl.gov/Geneways/GeneWays.html

System for automatically extracting, analzying, visualizing and integrating molecular pathway data from the research literature. System focuses on interactions between molecular substances and actions, providing a graphical consensus view on the collected information. GeneWays is designed as open platform, allowing researchers to query, review and critique integrated information.

Proper citation: GeneWays (RRID:SCR_000572) Copy   

•   Source: SciCrunch Registry

http://www.ascidiancenter.ucsb.edu/index.html

Supplier of Ciona (C. robusta and C. savignyi) adults and stable transgenic animals expressing tissue-specific fluorescent proteins for research laboratories. This ascidian culturing facility is located at the marine laboratory of the University of California at Santa Barbara (UCSB).

Proper citation: Ascidian Stock Center (ASC) (RRID:SCR_014949) Copy   

•   Source: SciCrunch Registry