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https://kmplot.com/analysis/

Web based survival analysis tool tailored for medical research. Used to assess correlation between expression of all genes (mRNA, miRNA, protein) and survival in samples from tumor types including breast, ovarian, lung, gastric, colon cancer, AML, and myeloma.

Proper citation: Kaplan Meier Plotter (RRID:SCR_024521) Copy   

•   Source: SciCrunch Registry
  

https://www.jenoptik.com/products/cameras-and-imaging-modules/microscope-cameras/progres-usb-20-firewire/software-download-progres

Software tool for image acquisition.Supports ProgRes microscope cameras and delivers optimal image quality and reproducible results.Included with all of Jenoptik ProgRes microscope cameras.

Proper citation: ProgRes Capture Pro (RRID:SCR_024489) Copy   

•   Source: SciCrunch Registry
  

http://madoka.denglab.org/

Web server as ultra fast approach for large scale protein structure similarity searching.The upload protein structure file should be in PDB format. Used for searching similar protein structures by aligning input structure with the whole PDB library.

Proper citation: MADOKA (RRID:SCR_024522) 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://sedfitsedphat.nibib.nih.gov/software/default.aspx

Software tool for analytical ultracentrifugation developed by Dynamics of Macromolecular Assembly group of Laboratory of Cellular Imaging and Macromolecular Biophysics, National Institute of Biomedical Imaging and Bioengineering, NIH. Used for biophysical analysis of macromolecular assembly.

Proper citation: SEDFIT (RRID:SCR_018365) Copy   

•   Source: SciCrunch Registry
  

https://github.com/blackrim/phyutility

Command line program that performs analyses or modifications on both trees and data matrices. Software phyloinformatics tool for trees, alignments and molecular data. Used for summarizing and manipulating phylogenetic trees, manipulating molecular data and retrieving data from NCBI.

Proper citation: Phyutility (RRID:SCR_018545) Copy   

•   Source: SciCrunch Registry
  

http://www.prisma-statement.org/

Evidence based minimum set of items for reporting in systematic reviews and meta analyses. Focuses on reporting of reviews evaluating randomized trials, but can also be used as basis for reporting systematic reviews of other types of research, particularly evaluations of interventions.

Proper citation: PRISMA (RRID:SCR_018721) Copy   

•   Source: SciCrunch Registry
  

http://bioinf.wehi.edu.au/software/elda/

Software tool for limiting dilution analysis, with particular attention to needs of stem cell assays. Provides confidence intervals for all LDA data sets, including those with 0% or 100% responses. Other features include test of adequacy of single hit hypothesis, tests for frequency differences between multiple data sets, and ability to take advantage of cases where number of cells in sample is counted exactly.

Proper citation: ELDA (RRID:SCR_018933) Copy   

•   Source: SciCrunch Registry
  

https://www.ebi.ac.uk/thornton-srv/software/PROCHECK/

Software tool to check stereochemical quality of protein structures. Its outputs comprise number of plots in PostScript format and comprehensive residue by residue listing. Includes PROCHECK-NMR for checking quality of structures solved by NMR.

Proper citation: PROCHECK (RRID:SCR_019043) Copy   

•   Source: SciCrunch Registry
  

https://cran.r-project.org/web/packages/igraph/

Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus.

Proper citation: igraph (RRID:SCR_019225) Copy   

•   Source: SciCrunch Registry
  

https://www.openclinica.com/

Web platform for electronic data capture by OpenClinica, LLC. Used as clinical trial management system.

Proper citation: OpenClinica (RRID:SCR_019223) Copy   

•   Source: SciCrunch Registry
  

http://shiny.chemgrid.org/boxplotr/

Web tool written in R for generation of box plots with R packages shiny, beanplot4, vioplot, beeswarm and RColorBrewer, and hosted on shiny server to allow for interactive data analysis. Data are held temporarily and discarded as soon as session terminates.Represents both summary statistics and distribution of primary data. Enables visualization of minimum, lower quartile, median, upper quartile and maximum of any data set.Data matrix can be uploaded as file or pasted into application. May be downloaded to run locally or as virtual machine for VMware and VirtualBox.

Proper citation: BoxPlotR (RRID:SCR_015629) Copy   

•   Source: SciCrunch Registry
  

https://bioconductor.org/packages/release/bioc/html/oligo.html

Software package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

Proper citation: oligo (RRID:SCR_015729) Copy   

•   Source: SciCrunch Registry
  

http://www.softgenetics.com/GeneMarker.php

Genotype analysis software which enhances the speed, accuracy, and ease of analysis. The software is an alternative to Applied BioSystems Genotyper®, GeneScan®, and other genotype analysis software.

Proper citation: GeneMarker (RRID:SCR_015661) Copy   

•   Source: SciCrunch Registry
  

http://phobius.sbc.su.se/

Web application for combined transmembrane topology and signal peptide prediction. Used for whole genome annotation of signal peptides and transmembrane regions. Predictor is based on hidden Markov model (HMM) that models different sequence regions of signal peptide and different regions of transmembrane protein in series of interconnected states.

Proper citation: Phobius (RRID:SCR_015643) Copy   

•   Source: SciCrunch Registry
  

https://genome.tugraz.at/genesisclient/genesisclient_description.shtml

Software for cluster analysis of microarray data. Genesis is a platform independent Java package of tools to simultaneously visualize and analyze a whole set of gene expression experiments.

Proper citation: Genesis (RRID:SCR_015775) Copy   

•   Source: SciCrunch Registry
  

http://molevol.cmima.csic.es/castresana/Gblocks_server.html

Software that eliminates poorly aligned positions and divergent regions of a DNA or protein alignment so that it becomes more suitable for phylogenetic analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Gblocks (RRID:SCR_015945) Copy   

•   Source: SciCrunch Registry
  

https://github.com/CAMI-challenge/AMBER

Software toolkit for the comparative assessment of genome reconstructions from metagenome benchmark datasets. It provides performance metrics, results rankings, and comparative visualizations for assessing multiple programs or parameter effects.

Proper citation: AMBER (RRID:SCR_016151) Copy   

•   Source: SciCrunch Registry
  

https://www.denovosoftware.com/?gclid=EAIaIQobChMI36rn3-Dd3AIV2ud3Ch27lw2oEAAYASAAEgLbRvD_BwE

Software tool for flow and image cytometry data analysis by De Novo Software company.

Proper citation: FCS Express (RRID:SCR_016431) Copy   

•   Source: SciCrunch Registry
  

https://www.ncbi.nlm.nih.gov/Web/Newsltr/Spring04/blastlab.html

Software tool as a program within the standalone BLAST package used to cluster either protein or nucleotide sequences. Used to make non redundant sequence sets.

Proper citation: BLASTClust (RRID:SCR_016641) Copy   

•   Source: SciCrunch Registry