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http://www.phidot.org/software/mark/background/
Software tool to provide parameter estimates from marked animals when they are re-encountered at later time, to create population size estimates. Used for analysis of data from marked individuals.
Proper citation: Program MARK (RRID:SCR_019281) Copy
https://github.com/bgcarlisle/Numbat
Software tool for managing extraction of large volumes of data from primary sources among multiple users, and then reconciling differences between them. Designed for use in systematic review projects in academic context.
Proper citation: Numbat (RRID:SCR_019207) Copy
https://galactic.biorelate.com
Platform of Biorelate to all auto curated data captured from millions of textual articles. Galactic lets you build intuitive queries and explore results through different views that best suit your research needs.Used by pharmaceutical and biotech companies to explore auto curated knowledge from millions of text sources, revealing hidden insights that might otherwise be lost.
Proper citation: Galactic (RRID:SCR_019208) Copy
https://bioconductor.org/packages/variancePartition/
Software R package to quantify and interpret divers of variation in multilevel gene expression experiments.Provides statistical and visualization framework for studying drivers of variation in RNA-seq datasets in many types of high throughput genomic assays including RNA-seq gene-, exon- and isoform-level quantification, splicing efficiency, protein quantification, metabolite quantification, metagenomic assays, methylation arrays and epigenomic sequencing assays.
Proper citation: variancePartition (RRID:SCR_019204) Copy
https://www.brainlatam.com/knowledge-base/brainvision-pycorder-installation-262
Open source acquisition program, based on Python programming language, for setting up BrainVision actiCHamp amplifier and storing data.
Proper citation: BrainVision PyCorder (RRID:SCR_019286) Copy
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
http://metagenomics.iiserb.ac.in/mp3/
Software tool for prediction of pathogenic proteins in genomic and metagenomic data. Used for identification of partial pathogenic proteins predicted from short (100-150 bp) metagenomic reads and also performs on complete protein sequences., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: MP3 tool (RRID:SCR_019282) Copy
https://labsn.github.io/expyfun/index.html
Auditory and visual stimulus delivery library for psychoacoustics in Python.
Proper citation: Expyfun (RRID:SCR_019285) Copy
https://CRAN.R-project.org/package=gbs2ploidy
Software R package as functions for inference of ploidy from Genotyping By Sequencing data, including function to infer allelic ratios and allelic proportions in Bayesian framework.
Proper citation: gbs2ploidy (RRID:SCR_019290) Copy
https://qiwei.shinyapps.io/PredictCOVID19/
Web app to help assess both short- and long-term forecasts of COVID-19 across the United States at multiple levels. Done by implementing one time-series model (ARIMA), one compartmental models (basic SIR), and six classical growth models, which all yield satisfactory prediction results in the past and current pandemics at early stage.
Proper citation: BayesEpiModels Web App (RRID:SCR_019292) Copy
https://github.com/pavanvidem/chira
Software tool suite to analyze RNA-RNA interactome experimental data such as CLASH, CLEAR-CLIP, PARIS, SPLASH, etc.
Proper citation: ChiRA (RRID:SCR_019219) Copy
Web application for visualisation of information derived from residue contact predictions in combination with other sources of information, such as secondary structure predictions, transmembrane helical topology, sequence conservation.Provides interactive interface for researchers in field of protein bioinformatics that are interested in analysing data on given protein.
Proper citation: ConPlot (RRID:SCR_019216) Copy
https://github.com/bgcarlisle/TRNscreener
Software tool as R script to provide function that takes two arguments: path to folder of plain text files named by their DOI, and output filename. For each file in folder, it searches for trial identifiers based on regex matching and writes CSV that contains all trial registration numbers and in case of ClinicalTrials.gov entries, whether they correspond to registry entry on ClinicalTrials.gov.
Proper citation: Trial Registration Number screener (RRID:SCR_019211) Copy
Online SPE System automates solid phase extraction to enrich analytes, remove matrix components or lower detection limits.
Proper citation: Agilent: 1290 Infinity II Online SPE System (RRID:SCR_019380) Copy
https://www.agilent.com/en/products/atomic-absorption/atomic-absorption-systems/240z-aa
Atomic Absorption System is used for detection limits and analyzes difficult matrices.
Proper citation: Agilent: 240Z AA Atomic Absorption System (RRID:SCR_019385) Copy
Preparative LC/MSD System enables high throughput purification and delivers high quality compounds.
Proper citation: Agilent: 1290 Infinity II Preparative LC/MSD System (RRID:SCR_019381) Copy
https://www.agilent.com/en/products/mp-aes/mp-aes-systems/4100-mp-aes
Discontinued Superseded by 4210 MP AES System.
Proper citation: Agilent: 4100 MP-AES (RRID:SCR_019390) Copy
https://bioconductor.org/packages/synergyfinder/
Software R package as efficient implementations for all popular synergy scoring models for drug combinations, including HSA, Loewe, Bliss and ZIP and visualization of synergy scores as either two dimensional or three dimensional interaction surface over dose matrix. Used to calculate and visualize synergy scores for drug combinations.
Proper citation: SynergyFinder (RRID:SCR_019318) Copy
https://www.agilent.com/en/products/mp-aes/mp-aes-systems/4200-mp-aes
High sensitivity atomic emission spectrometer. MP-AES Instrument utilizes microwave plasma and as it runs on air instead of combustible gases, it can be installed in either centralized laboratory or remote location. Detection limits down to ppb levels and no sample pretreatment necessary.
Proper citation: Agilent: 4200 MP-AES (RRID:SCR_019396) Copy
https://www.agilent.com/en/products/atomic-absorption/atomic-absorption-systems/240fs-aa
Atomic Absorption System determines the concentration of all elements from a single aspiration.
Proper citation: Agilent: 240FS AA Atomic Absorption System (RRID:SCR_019397) Copy
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