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https://geopandas.org/en/stable/

Software open-source Python library that makes it easy to work with geospatial data. It extends the popular data analysis library, Pandas, by allowing you to perform spatial operations on geometric shapes like points, lines, and polygons.

Proper citation: GeoPandas (RRID:SCR_028590) Copy   

•   Source: SciCrunch Registry

https://pypi.org/project/pip/

Software package installer for Python. You can use pip to install packages from the Python Package Index and other indexes.

Proper citation: pip (RRID:SCR_028591) Copy   

•   Source: SciCrunch Registry

https://github.com/openvax/mhcflurry

Software MHC I ligand prediction package with competitive accuracy and documented implementation. Used for peptide-MHC I binding affinity prediction.

Proper citation: mhcflurry (RRID:SCR_028577) Copy   

•   Source: SciCrunch Registry

https://github.com/VanLoo-lab/ASCAT.sc

Software application as implementation of ASCAT allowing generation of CNV profiles from single cell and short coverage sequencing data.

Proper citation: ASCAT sc (RRID:SCR_028613) Copy   

•   Source: SciCrunch Registry

https://github.com/markowetzlab/CINSignatureQuantification

Software R package to quantify the activity of signatures of chromosomal instability from absolute copy number profiles. Used to quantifying copy number signatures from absolute copy number profiles.

Proper citation: CINSignatureQuantification (RRID:SCR_028614) Copy   

•   Source: SciCrunch Registry

https://lume.tv/PANGEA/

Spacial neuron gene expression atlas. Interactive, server-free web application and spatial transcriptomics database designed to help researchers map and analyze gene expression within the brain. Mouse whole brain spatial transcriptomic atlas.

Proper citation: PANGEA (RRID:SCR_028559) Copy   

•   Source: SciCrunch Registry

http://babylone.ulb.ac.be/BeAtMuSiC/

Web tool for prediction of changes in protein-protein binding affinity on mutations. Predictor of changes in binding free energy induced by point mutations. It relies on a set of statistical potentials derived from known protein structures, and combines the effect of the mutation on the strength of the interactions at the interface, and on the overall stability of the complex.

Proper citation: BeAtMuSiC (RRID:SCR_028562) Copy   

•   Source: SciCrunch Registry

http://www.msstate.edu/

Public university in Mississippi with land, sea and space grants that offers degree programs in areas such as agriculture and applied sciences at the undergraduate and graduate levels.

Proper citation: Mississippi State University; Mississippi; USA (RRID:SCR_000361) Copy   

•   Source: SciCrunch Registry

https://code.google.com/p/taps/

A bioinformatic tool for the identification of allele-specific copy numbers in tumor samples using data from Affymetrix SNP arrays.

Proper citation: TAPS (RRID:SCR_000356) Copy   

•   Source: SciCrunch Registry

http://sydney.edu.au/

A public research university in Sydney, Australia that offers a wide range of degree programs at the undergraduate and graduate level.

Proper citation: University of Sydney; Sydney; Australia (RRID:SCR_000381) Copy   

•   Source: SciCrunch Registry

http://bioinformatics.research.nicta.com.au/software/is-rsnp/

Software tool that predicts whether a single nucleotide polymorphism (SNP) is a regulatory SNP (rSNP). For a given SNP, and using a statistical framework, it can successfully predict the set of transcription factors (TFs) for which binding is affected. The algorithm provides the statistical power to scan large numbers of SNPs, making it suitable to use to screen all associated SNPs output by a typical genome-wide association studies (GWAS).

Proper citation: is-rSNP (RRID:SCR_000387) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/as-peak/

A software that utilizes a peak detection algorithm to identify RNA-protein binding sites.

Proper citation: AS-Peak (RRID:SCR_000380) Copy   

•   Source: SciCrunch Registry

http://sourceforge.net/projects/genseng/

Software for detecting copy number variations from next generation sequencing data. Used to identify regions of discrete copy number changes while simultaneously accounting for effects of multiple confounders.

Proper citation: GENSENG (RRID:SCR_000378) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowFlowJo.html

A Bioconductor package that can import gates defined by the commercial package FlowJo and work with them in a manner consistent with the other flow packages in Bioconductor. FlowJo is a commercial GUI based software package from TreeStar Inc. for the visualization and analysis of flow cytometry data. One of the FlowJo standard export file types is the FlowJo Workspace. This is an XML document that describes files and manipulations that have been performed in the FlowJo GUI environment. This package can take apart the FlowJo workspace and deliver the data into R in the flowCore paradigm.

Proper citation: flowFlowJo (RRID:SCR_000410) Copy   

•   Source: SciCrunch Registry

http://www.utdallas.edu/

A public research university in Texas that offers degree programs in engineering, business, political science and the natural sciences at the undergraduate and graduate levels. The university also houses research that focuses on space science, bioengineering, cybersecurity, nanotechnology, and behavioral and brain sciences.

Proper citation: University of Texas at Dallas; Texas; USA (RRID:SCR_000375) Copy   

•   Source: SciCrunch Registry

https://www.bdbiosciences.com/documents/FACSCalibur_FlowCytometry_TechSpec.pdf

Automated benchtop flow cytometry system. It allows measuring four fluorochrome-conjugates, forward and side scatter., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: BD Biosciences: FACSCalibur Flow Cytometry System (RRID:SCR_000401) Copy   

•   Source: SciCrunch Registry

http://www.omicia.com/products/opal-research

Software which integrates a comprehensive, automated genome annotation engine with the VAAST and Phevor disease gene prioritization tools to rank gene variants on the severity of their impact on protein function and likelihood to cause disease. Each variant in a gene is analyzed for its impact on protein function, conservation and frequency. Each gene is ranked rather than filtered in order to ensure critical targets are not prematurely removed.

Proper citation: Opal Research (RRID:SCR_000405) Copy   

•   Source: SciCrunch Registry

http://www.dnastar.com/t-seqmanpro.aspx

Software for analysis and DNA sequence assembly of Sanger data. It also provides visualizations and analysis of next-gen projects assembled by SeqMan NGen.

Proper citation: Lasergene's SeqMan Pro (RRID:SCR_000283) Copy   

•   Source: SciCrunch Registry

http://www.irfanview.com/

An open source graphic viewer. Some features include batch conversion, paint options, basic editing and several supported file formats. It is compatible with Windows 9x, ME, NT, 2000, XP, 2003 , 2008, Vista, Windows 7, Windows 8, and Windows 10.

Proper citation: IrfanView (RRID:SCR_000315) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/packages/release/bioc/html/flowStats.html

Software using statistical methods and functionality to analyze flow data that is beyond the basic infrastructure provided by the flowCore package.

Proper citation: flowStats (RRID:SCR_000399) Copy   

•   Source: SciCrunch Registry