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http://csb.pitt.edu/erc_analysis/Methods.php

Web-based statistical application that measures correlated rates across a phylogeny, allowing for extraction of genes with similar evolutionary histories. It can identify new functional connections between genes.

Proper citation: Evolutionary Rate Covariation (RRID:SCR_015669) Copy   

•   Source: SciCrunch Registry

https://portals.broadinstitute.org/cmap/

Collection of genome-wide transcriptional expression data from cultured human cells treated with bioactive small molecules and simple pattern-matching algorithms. camp aims to enable the discovery of functional connections between drugs, genes and diseases through the transitory feature of common gene-expression changes., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Connectivity Map 02 (RRID:SCR_015674) Copy   

•   Source: SciCrunch Registry

https://github.com/hpardoe/napr/

Cloud-based framework that allows users to estimate the age of individual subjects using cortical thickness maps derived from their own locally processed T1-weighted whole brain MRI scans. The provided age prediction models were trained using (i) relevance vector machines and (ii) Gaussian processes machine learning methods applied to cortical thickness surfaces obtained using Freesurfer v5.3.

Proper citation: NAPR: Neuroanatomical Age Prediction using R (RRID:SCR_015759) Copy   

•   Source: SciCrunch Registry

https://github.com/DDTBOX/DDTBOX

Software toolkit for multivariate pattern analysis (MVPA) of event-related potentials. This software is written in MATLAB.

Proper citation: Decision Decoding Toolbox (RRID:SCR_015978) Copy   

•   Source: SciCrunch Registry

http://www.braincode.ca

Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.

Proper citation: Brain-CODE (RRID:SCR_015877) Copy   

•   Source: SciCrunch Registry

https://pdb-dev.wwpdb.org

Data repository for integrative/hybrid structural models of macromolecules and their assemblies. This includes atomistic models as well as multi-scale models consisting of different coarse-grained representations.

Proper citation: PDB-Dev (RRID:SCR_016185) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=simr

Software R package for power analysis of generalized linear mixed models by simulation. Used to calculate power for generalised linear mixed models.

Proper citation: SIMR (RRID:SCR_019287) Copy   

•   Source: SciCrunch Registry

https://CRAN.R-project.org/package=spdep

Software R package as collection of functions to create spatial weights matrix objects from polygon contiguities, from point patterns by distance and tessellations, for summarizing these objects, and for permitting their use in spatial data analysis, including regional aggregation by minimum spanning tree.

Proper citation: spdep (RRID:SCR_019294) Copy   

•   Source: SciCrunch Registry

https://github.com/Danis102/seqpac

Software R package for analysis of short sequenced reads. Framework for small RNA analysis in R using Sequence Based Counts.Can be applied on any type of data generated by large scale nucleotide sequencing, where user wish to maintain sequence integrity during whole analysis.

Proper citation: seqpac (RRID:SCR_021079) Copy   

•   Source: SciCrunch Registry

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https://biology-assets.anu.edu.au/GenAlEx/Welcome.html

Software tool as cross platform package for population genetic analyses that runs within Microsoft Excel. Offers analysis of diploid codominant, haploid and binary genetic loci and DNA sequences.Originally developed as teaching tool to facilitate teaching population genetic analysis at graduate level.

Proper citation: GenAlEx (RRID:SCR_021102) Copy   

•   Source: SciCrunch Registry

https://www.waters.com/waters/en_US/High-Definition-Imaging-(HDI)-Software/nav.htm?cid=134833914&locale=en_US

Software package contains data analysis and processing tools required for rapid and effective interrogation of imaging data. Allows for full integration of full spectrum molecular imaging experiments on SYNAPT family platforms, as well as DESI imaging on Xevo G2-XS QTof Mass Spectrometers, using single user interface.

Proper citation: Waters High Definition Imaging (RRID:SCR_021054) Copy   

•   Source: SciCrunch Registry

https://github.com/bahanonu/ciatah

Software package for analyzing one and two photon calcium imaging datasets.Can be used to create GUI-less, command line ready analysis pipelines. Supports Neurodata Without Borders data standard for reading/writing cell-extraction (e.g. outputs of PCA-ICA, CELLMax, CNMF, CNMF-E, EXTRACT, etc.). Supports reading and writing NWB movie files with continued integration planned. Supports most major imaging movie file formats: HDF5, NWB, AVI, ISXD [Inscopix], and TIFF.

Proper citation: calciumImagingAnalysis (RRID:SCR_021153) Copy   

•   Source: SciCrunch Registry

https://github.com/parkgilbong/Minhee_Analysis_Pack

Software package for detection and measurement of spontaneous synaptic events. Integrated software package for detection and management of spontaneous synaptic events. Used in neurophysiology to detect spontaneous postsynaptic currents, search and visualize them in custom way, and perform hypothesis testing of retrieved data.

Proper citation: Minhee Analysis Package (RRID:SCR_021250) Copy   

•   Source: SciCrunch Registry

https://github.com/YttriLab/B-SOID

Software pipeline that pairs unsupervised pattern recognition with supervised classification to achieve fast predictions of behaviors that are not predefined by users.Unsupervised learning algorithm that discovers and classifies actions based on inherent statistics of data points provided.

Proper citation: Behavioral Segmentation of Open-field in DeepLabCut (RRID:SCR_021385) Copy   

•   Source: SciCrunch Registry

https://github.com/jonnew/Oat

Software tool as real time position tracker for behavioral research. Used for processing images, extracting object position information, and streaming data to disk and/or the network in real time.

Proper citation: Online Animal Tracker (RRID:SCR_021412) Copy   

•   Source: SciCrunch Registry

https://www.research.va.gov/mvp/

National research program to learn how genes, lifestyle, and military exposures affect health and illness.

Proper citation: Million Veteran Program (RRID:SCR_021731) Copy   

•   Source: SciCrunch Registry

https://samplesizeshop.org

Platform for multilevel and longitudinal data.Provide researchers such as behavioral and social scientists with tools and education related to study design including Calculating power and sample size for any univariate or multivariate test for general linear multivariate model, assuming fixed predictors;Producing confidence intervals on power estimates for designs with fixed predictors;Producing power calculations for designs with single Gaussian covariate;Supporting designs with unequal group sizes, and complicated covariance structures;Creating basic power curves.

Proper citation: Sample Size Shop (RRID:SCR_021747) Copy   

•   Source: SciCrunch Registry

https://trialdesign.org/

Integrated platform for designing clinical trials.

Proper citation: Trialdesign (RRID:SCR_021749) Copy   

•   Source: SciCrunch Registry

https://www.microns-explorer.org/

Portal to release connectivity and functional imaging data collected by consortium of laboratories led by groups at Allen Institute for Brain Science, Princeton University, and Baylor College of Medicine, with support from broad array of teams, coordinated and funded by IARPA MICrONS program. Data include large scale electron microscopy based reconstructions of cortical circuitry from mouse visual cortex, with corresponding functional imaging data from those same neurons.

Proper citation: Microns Explorer (RRID:SCR_021678) Copy   

•   Source: SciCrunch Registry

https://github.com/bioinfo-biols/CIRIquant

Software Python package for accurate circRNA quantification and differential expression analysis. Comprehensive analysis pipeline for circRNA detection and quantification in RNA-Seq data. Accurate quantification of circular RNAs identifies extensive circular isoform switching events.

Proper citation: CIRIquant (RRID:SCR_021661) Copy   

•   Source: SciCrunch Registry