Tools   Select Another Resource Report Type

https://github.com/Griffan/FASTQuick

Software tool for rapid and comprehensive quality assessment of raw sequence reads. It generates comprehensive list of QC statistics, including ancestry and contamination estimation.

Proper citation: FASTQuick (RRID:SCR_019269) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/fgsea/

Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.

Proper citation: fgsea (RRID:SCR_020938) Copy   

•   Source: SciCrunch Registry

https://www.autodesk.com/products/netfabb/overview?plc=F360NFP&term=1-YEAR&support=ADVANCED&quantity=1

Software tool to open and assess stereolithographic data. Software application tailored for additive manufacturing, rapid prototyping, and 3D printing.

Proper citation: Autodesk Netfabb Premium (RRID:SCR_019812) Copy   

•   Source: SciCrunch Registry

https://gitlab.com/PAM-PIE/PAM

Software package for quantitative analysis of fluorescence microscopy and spectroscopy data, with focus on experiments using pulsed interleaved excitation. Open source software package written in MATLAB that offers workflow through its graphical user interface. Framework for integrated analysis of imaging, single-molecule, and ensemble fluorescence data.Supports most types of data collection modalities.

Proper citation: PAM (RRID:SCR_020966) Copy   

•   Source: SciCrunch Registry

https://www.bmglabtech.com/mars-data-analysis-software/

Proprietary software package for data analysis by BMG Labtech.

Proper citation: MARS Data Analysis Software (RRID:SCR_021015) Copy   

•   Source: SciCrunch Registry

http://synaptosoft.com/MiniAnalysis/ABFUtility.html

Software tool to convert data files from Mac program such as Igor and Pulse or John Dempster CDR, WinTida, to ABF formats and analyze them with Mini Analysis Program.

Proper citation: ABF Utility (RRID:SCR_019222) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://www.miltenyibiotec.com/products/macs-flow-cytometry/software/flowlogic-software.html

Software tool for flow cytometry data analysis by Miltenyi Biotec.

Proper citation: Flowlogic (RRID:SCR_020942) Copy   

•   Source: SciCrunch Registry

https://sydneybiox.github.io/CiteFuse/

Software R package consisting of suite of tools for doublet detection, modality integration, clustering, differential RNA and protein expression analysis, antibody-derived tag evaluation, ligand-receptor interaction analysis and interactive web-based visualization of CITE-seq data.

Proper citation: CiteFuse (RRID:SCR_019321) Copy   

•   Source: SciCrunch Registry

https://cgmaptools.github.io

Software package for DNA methylation analysis. Used for context-wise, gene-wise, bin-wise, region-wise and sample-wise analysis and visualizations. Used to improve precision of heterozygous SNV calls and supports allele-specific methylation detection and visualization in bisulfite-sequencing data.

Proper citation: cgmapotools (RRID:SCR_020950) Copy   

•   Source: SciCrunch Registry

https://pubmed.ncbi.nlm.nih.gov/24356771/

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on March 15, 2021. Software tool for analysis of cross-linked peptides.

Proper citation: xProhet (RRID:SCR_021005) Copy   

•   Source: SciCrunch Registry

https://satijalab.org/signac/index.html

Software framework for analysis of single cell chromatin data. Used for analysis, interpretation, and exploration of single cell chromatin datasets including datasets that co-assay DNA accessibility with gene expression, protein abundance, and mitochondrial genotype. Analysis of single-cell chromatin data including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis, and interactive visualization.

Proper citation: Signac (RRID:SCR_021158) Copy   

•   Source: SciCrunch Registry

https://www.fluidigm.com/singlearticles/cytof-software-upgrade-7dot0

Software for analyzing mass cytometry (CyTOF) data.

Proper citation: Fluidigm CyTOF (RRID:SCR_021055) Copy   

•   Source: SciCrunch Registry

https://github.com/gordonberman/MotionMapper

Software tool to work on videos (not poses).Uses image analysis and multivariate statistical methods to find stereotyped behaviors in flies, mice, and other species.

Proper citation: MotionMapper (RRID:SCR_021384) Copy   

•   Source: SciCrunch Registry

https://caiman.readthedocs.io/

Software Python toolbox for large scale calcium imaging data analysis and behavioral analysis.Used for motion correction, source extraction, spike deconvolution, and component registration across multiple days. It is suitable for both two-photon and one-photon fluorescence microscopy data, and can be run in both batch and online modes. Contains some routines for analysis of behavior from video cameras.

Proper citation: CaImAn (RRID:SCR_021152) Copy   

•   Source: SciCrunch Registry

https://github.com/tseemann/abricate

Software tool for mass screening of contigs for antimicrobial and virulence genes. Mass screening of contigs for antimicrobial resistance or virulence genes. It comes bundled with multiple databases: NCBI, CARD, ARG-ANNOT, Resfinder, MEGARES, EcOH, PlasmidFinder, Ecoli_VF and VFDB.

Proper citation: Abricate (RRID:SCR_021093) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/us/en/home/technical-resources/software-downloads/expressionsuite-software.html

Software tool to quantify relative gene expression across large number of genes and samples. Allows to analyze gene expression data on any current Applied Biosystems real time PCR instrument.

Proper citation: ExpressionSuite (RRID:SCR_021095) Copy   

•   Source: SciCrunch Registry

http://www.processmacro.org

Software tool as macro for SPSS, SAS, and R that conducts observed variable mediation, moderation, and conditional process analysis.Observed variable OLS and logistic regression path analysis modeling tool. Used for estimating direct and indirect effects in single and multiple mediator models parallel and serial, two and three way interactions in moderation models along with simple slopes and regions of significance for probing interactions, and conditional indirect effects in moderated mediation models with single or multiple mediators or moderators. Operates on Windows and Mac versions of SPSS and SAS.

Proper citation: PROCESS (RRID:SCR_021369) Copy   

•   Source: SciCrunch Registry

http://bioinf.wehi.edu.au/limma/

Software package for the analysis of gene expression microarray data, especially the use of linear models for analyzing designed experiments and the assessment of differential expression.

Proper citation: LIMMA (RRID:SCR_010943) Copy   

•   Source: SciCrunch Registry

http://kissplice.prabi.fr/

Software tool that enables analysis of RNA-seq data with or without reference genome. Local transcriptome assembler for SNPs, indels and AS events.

Proper citation: KisSplice (RRID:SCR_011893) Copy   

•   Source: SciCrunch Registry