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http://spark.apache.org/

Software tool as a unified analytics engine for large scale data processing. An open source distributed general purpose cluster computing framework.

Proper citation: Apache Spark (RRID:SCR_016557) Copy   

•   Source: SciCrunch Registry

https://github.com/facebook/prophet

Open source software package for producing forecasts for time series data that has multiple seasonality with linear or non linear growth. Implemented in R or Phyton.

Proper citation: Prophet (RRID:SCR_017083) Copy   

•   Source: SciCrunch Registry

http://databiosphere.org

Project whose goal is to provide Data Environments to the biomedical community. The Data Biosphere works to create a user experience around key modular components — each having discrete capabilities and clear rules of interaction, and each served by multiple alternative implementations.

Proper citation: Data Biosphere (RRID:SCR_016154) Copy   

•   Source: SciCrunch Registry

http://reproducibility.stanford.edu/

Center with the goal of harnessing high-performance computing to make neuroscience research more reliable.Provide researchers with tools to analyze their data in ways that focus on the reproducibility of the results through the OpenfMRI ( OpenNeuro ) and Neurovault projects.

Proper citation: Stanford Center for Reproducible Neuroscience (RRID:SCR_016684) Copy   

•   Source: SciCrunch Registry

https://github.com/TeamMacLean/atacr

Software that analyzes count data from RNA-capture-seq and ATAC-capture-seq experiments. Using BioConductor RangedSummarizedExperiment objects, atacr implements a set of helper functions and quality control plots specific to the analysis of counts of reads in windows across genomes.

Proper citation: atacr (RRID:SCR_016286) Copy   

•   Source: SciCrunch Registry

https://github.com/kstreet13/slingshot

Software R package for identifying and characterizing continuous developmental trajectories in single cell data. Cell lineage and pseudotime inference for single-cell transcriptomics.

Proper citation: Slingshot (RRID:SCR_017012) Copy   

•   Source: SciCrunch Registry

Ratings or validation data are available for this resource

https://github.com/BodenmillerGroup/imctools

Software Python package that implements preprocessing pipeline for imaging mass cytometry data. Can convert IMC raw files to tiff files that are used as inputs into CellProfiller, Ilastik, Fiji etc.

Proper citation: imctools (RRID:SCR_017132) Copy   

•   Source: SciCrunch Registry

https://github.com/colinvaz/nmf-toolbox

Software toolbox for performing Non-negative Matrix Factorization (NMF) and several variants. Used to factorize one non negative matrix into two non negative factors, that is basis matrix and coefficient matrix. Applied in bioinformatics as data mining approach.

Proper citation: NMF Toolbox (RRID:SCR_017069) Copy   

•   Source: SciCrunch Registry

https://drugs.ncats.io/

Portal of NCATS (the National Center for Advancing Translational Sciences) for drug development information including:US approved drugs, marketed drugs, investigational drugs. Provides manually curated data supplied by the FDA and private companies. Provides drugs marketing and regulatory status, drug ingredient definitions, biological activity and clinical use.

Proper citation: Inxight (RRID:SCR_016490) Copy   

•   Source: SciCrunch Registry

https://nels.bioinfo.no

Web portal for the administration of Norwegian e-Infrastructure for Life Sciences. Enables Norwegian life scientists and their international collaborators to store, share, archive, and analyse their genomics scale data. NeLS is one of the packages of the ELIXIR.NO project.

Proper citation: NeLS (RRID:SCR_016301) Copy   

•   Source: SciCrunch Registry

http://www.biosoft.com/w/assayzap.htm

Software tool as universal assay calculator for RIA, ELISA, IRMA, colorimetric or any other type of assay by Biosoft. Maintains record for each assay, and enables standard curve and QCs to be compared and adjusted. Can process data from 96 and 384-well plate readers in any order.

Proper citation: AssayZap (RRID:SCR_016991) Copy   

•   Source: SciCrunch Registry

https://www.ruhr-uni-bochum.de/mpc/software/ProCon/index.html.en

Java based conversion tool for conversion of data from Proteomics files or a LIMS (Laboratory Information Management System) database into standard formats. Used to support wet-lab scientists in creating proteomics data files ready for upload into the public repositories.

Proper citation: ProCon - PROteomics CONversion (RRID:SCR_016363) Copy   

•   Source: SciCrunch Registry

https://github.com/wdecoster/nanofilt

Software tool written in Python to perform its filtering based on mean read quality and GC content and read length. Used for filtering and trimming of long read sequencing data.

Proper citation: NanoFilt (RRID:SCR_016966) Copy   

•   Source: SciCrunch Registry

https://github.com/mandricigor/ScaffMatch

Software tool as scaffolding algorithm based on maximum weight matching able to produce high quality scaffolds from next generation sequencing data (reads and contigs). Able to handle reads with both short and long insert sizes.

Proper citation: ScaffMatch (RRID:SCR_017025) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/nicofmay/basta-bayesian-structured-coalescent-approximation/src/master/

Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations.

Proper citation: BASTA (RRID:SCR_017303) Copy   

•   Source: SciCrunch Registry

https://geomagic-studio.software.informer.com/12.0/

Software tool to convert 3D scans into parametric models. Transforms 3D scan data into highly accurate surface, polygon and native CAD models. Used for reverse engineering, product design, rapid prototyping and analysis.

Proper citation: GEOMAGIC Studio (RRID:SCR_016978) Copy   

•   Source: SciCrunch Registry

https://covid-19.ensembl.org/

Ensembl SARS-Cov2 data portal.

Proper citation: Ensembl Covid-19 (RRID:SCR_024704) Copy   

•   Source: SciCrunch Registry

https://cab.spbu.ru/software/spades/

Software package for assembling single cell genomes and mini metagenomes. Uses short read sets as input. Used for genomes of uncultivatable bacteria that vastly exceeds what may be obtained via traditional metagenomics studies. Works with Illumina or IonTorrent reads and can provide hybrid assemblies using PacBio, Oxford Nanopore and Sanger reads. Intended for small genomes like bacterial or fungal., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: SPAdes (RRID:SCR_000131) Copy   

•   Source: SciCrunch Registry

https://www.cdc.gov/fluview/?CDC_AAref_Val=https://www.cdc.gov/flu/weekly/weeklyarchives2008-2009/weekly15.htm

This page contains the Influenza Surveillance Report during 2008-2009 Influenza Season Week 15, ending April 18, 2009.

Proper citation: FluView: A Weekly Influenza Surveillance Report (RRID:SCR_001118) Copy   

•   Source: SciCrunch Registry

http://www.duke.edu/web/gpcr-assay/index.html

Describes data from and access to permanent cell lines containing beta-arrestin fluorescent protein biosensors. This assay Bank provides plasmids, cells lines, and resulting data to the NIDA/NIH funded research community in order to better understand and combat addiction.

Proper citation: Addiction Research GPCR Assay Bank (RRID:SCR_002895) Copy   

•   Source: SciCrunch Registry