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https://github.com/Gaius-Augustus/learnMSA

Software tool as multiple sequence alignment formulated as statistical machine learning problem, where optimal profile hidden Markov model for potentially very large family of protein sequences is searched and alignment is decoded.

Proper citation: learnMSA (RRID:SCR_022572) Copy   

•   Source: SciCrunch Registry

https://github.com/FunctionLab/sei-framework

Web server for systematically predicting sequence regulatory activities and applying sequence information to human genetics data. Provides global map from any sequence to regulatory activities, as represented by sequence classes, and each sequence class integrates predictions for chromatin profiles like transcription factor, histone marks, and chromatin accessibility profiles across wide range of cell types.

Proper citation: sei (RRID:SCR_022571) Copy   

•   Source: SciCrunch Registry

https://github.com/djamesbarker/pMAT

Open source software suite for analysis of fiber photometry data.

Proper citation: pMAT (RRID:SCR_022570) Copy   

•   Source: SciCrunch Registry

https://github.com/JinmiaoChenLab/Rphenograph

Software R tool as simple R implementation of PhenoGraph algorithm, which is clustering method designed for high dimensional single cell data analysis.

Proper citation: Rphenograph (RRID:SCR_022603) Copy   

•   Source: SciCrunch Registry

https://www.ibm.com/products/structural-equation-modeling-sem

Structural equation modeling software helping support your research and theories by extending standard multivariate analysis methods, including regression, factor analysis, correlation and analysis of variance.

Proper citation: IBM SPSS Amos (RRID:SCR_022686) Copy   

•   Source: SciCrunch Registry

https://quality-preclinical-data.eu/about-eqipd/eqipd-quality-system/

Preclinical research quality system that can be applied in public and private sectors to ensure that early drug development research proceeds along structured lines. Used for ensuring generation of reliable preclinical data. Proposes guidance on expectations for quality related measures, defines criteria for adequate processes like performance standards, and provides examples of how such measures can be developed and implemented. EQIPD certification was established by EQIPD consortium and is now managed by its legacy organisation GoEQIPD.

Proper citation: Enhancing Quality In Preclinical Data Quality System (RRID:SCR_022729) Copy   

•   Source: SciCrunch Registry

https://www.erim.eur.nl/research-support/meta-essentials/

Software tool for meta analysis. Facilitates integration and synthesis of effect sizes from different studies. Consists of set of workbooks designed for Microsoft Excel that automatically produces all required statistics, tables, figures, and more.

Proper citation: Meta Essentials (RRID:SCR_022464) Copy   

•   Source: SciCrunch Registry

http://splicing.cs.washington.edu/

Web tool to predict effects of sequence variants on alternative splicing. Predicts changes in alternative 5' splice events as well as skipped exon events.

Proper citation: Hexamer Additive Linear (RRID:SCR_022581) Copy   

•   Source: SciCrunch Registry

https://web.rniapps.net/netshift/

Web tool for identification of driver nodes between case control association networks.Methodology for understanding driver microbes from healthy and disease microbiome datasets.

Proper citation: NetShift (RRID:SCR_022733) Copy   

•   Source: SciCrunch Registry

https://upset.app/#:~:text=UpSet%20plots%20the%20intersections%20of,is%20part%20of%20an%20intersection.

Software tool to visualize set intersections in matrix layout. Interactive, web based visualization technique designed to analyze set based data. Visualizes both, set intersections and their properties, and elements in dataset. Used for quantitative analysis of data with more than three sets.

Proper citation: UpSet (RRID:SCR_022731) Copy   

•   Source: SciCrunch Registry

http://virtualplant.bio.nyu.edu/cgi-bin/vpweb/

Software platform to support systems biology research. Integrates genomic data and provides visualization and analysis tools for exploration of genomic data. Provides tools to generate biological hypotheses.

Proper citation: VirtualPlant (RRID:SCR_022576) Copy   

•   Source: SciCrunch Registry

https://github.com/im3sanger/dndscv

Software R package is group of maximum likelihood dN/dS methods designed to quantify selection in cancer and somatic evolution. Contains functions to quantify dN/dS ratios for missense, nonsense and essential splice mutations, at level of individual genes, groups of genes or at whole-exome level.Used to detect cancer driver genes on datasets ranging from few samples to thousands of samples, in whole-exome/genome or targeted sequencing studies.

Proper citation: dNdScv (RRID:SCR_023123) Copy   

•   Source: SciCrunch Registry

https://biccn.org/teams/u01-fischl

Project to develop and utilize imaging infrastructure to create human brain cell census and instantiate it in coordinate system that will enable immediate impact of all in vivo MRI studies of human brain. Consortium for creating cellular census of human cerebral cortex.

Proper citation: BICCN Imaging and analysis Techniques to Construct Cell Census Atlas of Human Brain (RRID:SCR_023000) Copy   

•   Source: SciCrunch Registry

https://github.com/AlexandrovLab/SigProfilerExtractor/

Software tool for de novo extraction of mutational signatures from data generated in matrix format. Identifies number of operative mutational signatures, their activities in each sample, and probability for each signature to cause specific mutation type in cancer sample.

Proper citation: SigProfilerExtractor (RRID:SCR_023121) Copy   

•   Source: SciCrunch Registry

https://pypi.org/search/?q=EmaCalc

Software package in Python for statistical analysis of Ecological Momentary Assessment data.

Proper citation: EmaCalc (RRID:SCR_022943) Copy   

•   Source: SciCrunch Registry

https://mriqc.readthedocs.io/en/latest/

Software tool as quality assurance workflow for Brain Imaging Data Structure compliant anatomical and functional MRI datasets. Used to extract no-reference image quality metrics from structural and functional magnetic resonance imaging data.

Proper citation: MRIQC (RRID:SCR_022942) Copy   

•   Source: SciCrunch Registry

https://cytotrace.stanford.edu/

Software tool that predicts differentiation state of cells from single cell RNA sequencing data. Used for predicting differentiation states from scRNA-seq data.

Proper citation: CytoTRACE (RRID:SCR_022828) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/DEP/

Software R package provides integrated analysis workflow for analysis of mass spectrometry proteomics data for differential protein expression or differential enrichment.

Proper citation: Differential Enrichment analysis of Proteomics data (RRID:SCR_023090) Copy   

•   Source: SciCrunch Registry

http://www.csbio.sjtu.edu.cn/bioinf/plant-multi/

Web application for predicting subcellular localization of plant proteins including those with multiple sites.Top Down Strategy to Augment Power for Predicting Plant Protein Subcellular Localization.

Proper citation: Plant mPLoc (RRID:SCR_023014) Copy   

•   Source: SciCrunch Registry

https://abi-services.informatik.uni-tuebingen.de/multiloc2/webloc.cgi

Web application for integrating phylogeny and Gene Ontology terms into subcellular protein colalization prediction.Extensive high performance subcellular protein localization prediction system.

Proper citation: Multi Loc2 (RRID:SCR_023013) Copy   

•   Source: SciCrunch Registry