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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://omictools.com/splicing-express-tool
Software suite for Alternative Splicing Events (ASEs) analysis from transcriptome sequencing data in any transcriptome. Used for identification, annotation and visualization. Written in Perl and suitable to run only in UNIX-like systems.
Proper citation: Splicing Express (RRID:SCR_016498) Copy
https://github.com/PF2-pasteur-fr/SARTools
Software package as a DESeq2- and EdgeR-Based R Pipeline for Comprehensive Differential Analysis of RNA-Seq Data.
Proper citation: SARTools (RRID:SCR_016533) Copy
http://saclab.tamu.edu/essentiality/transit/
Software tool Python based and open source for statistical analysis of TnSeq data. Provides a graphical interface to three different statistical methods for analyzing TnSeq data capable of identifying essential genes in individual datasets as well as comparative analysis between conditions.
Proper citation: TRANSIT (RRID:SCR_016492) Copy
https://github.com/cortex-lab/Kilosort
Software tool that implements an integrated template matching framework for detecting and clustering spikes from multi-channel electrophysiological recordings.
Proper citation: KiloSort (RRID:SCR_016422) Copy
http://bioinformatics.mdc-berlin.de/pigx/
Software application as a collection of genomic pipelines used for raw fastq read data of bisulfite experiments, RNAseq samples, single cell dropseq analysis, reads from ChIPseq experiments, analysis of sequence mutations in CRISPR-CAS9 targeted amplicon sequencing data.
Proper citation: PiGx (RRID:SCR_016476) Copy
Database of free scholary articles. Content from over 50,000 publishers and repositories easy to find, track, and use. A website featuring web-based tools created and maintained by Impactstory, Inc.
Proper citation: Unpaywall (RRID:SCR_016471) Copy
Software tool for microarray analysis designed for biologists . Used for identification of differential expression by providing interactive visualizations.
Proper citation: Transcriptome Analysis Console (RRID:SCR_016519) Copy
http://www.dhal.com/viewboxindex.htm
Software for cephalometric analysis. Customizable. Allows rendering, viewing and measuring of 3D data from CT scanners. Used in orthodontic departments for analysis of the dental and skeletal relationships of a human skull.
Proper citation: Viewbox4, Cephalometric software (RRID:SCR_016481) Copy
http://www.eulerdiagrams.org/eulerAPE/
Software that uses ellipses to automatically draw accurate area-proportional Venn diagrams for 3-set data. It generates an exact diagram for most of the cases, and when it fails, the best diagram obtained through the hill climbing search is displayed, together with the inaccuracy values for each region.
Proper citation: eulerAPE (RRID:SCR_016457) Copy
https://cran.r-project.org/web/packages/dplyr/index.html
Software tool for working with data frame like objects, both in memory and out of memory. It is a grammar of data manipulation, providing a consistent set of verbs that help you solve the most common data manipulation challenges: mutate, select, filer, summerise, arrange.
Proper citation: dplyr (RRID:SCR_016708) Copy
Software package to detect and quantify local splicing variations (LSV) from RNA-Seq data. Used to automatically detect and downweight outliers in RNA-Seq datasets with replicates for differential splicing (SD) analysis.
Proper citation: MAJIQ (RRID:SCR_016706) Copy
Portal for sharing spinal cord injury data from basic and clinical research to promote transparency, rigor and reproducibility. Community based repository for spinal cord injury research.
Proper citation: Open Data Commons for Spinal Cord Injury (RRID:SCR_016673) Copy
https://github.com/CPernet/brain_colours
Software tool as a perceptually uniform color maps. Used in scientific literature to reflect data of brain imaging.
Proper citation: Colour maps for brain imaging (RRID:SCR_016715) Copy
https://cran.r-project.org/web/packages/anocva/index.html
Software R package as a nonparametric statistical test to compare clustering structures with applications in functional magnetic resonance imaging data (fMRI). Used for analysis of cluster variability in the diagnosis of neuropsychological disorders.
Proper citation: ANOCVA (RRID:SCR_016719) Copy
https://www.ncbi.nlm.nih.gov/geo/info/geo2r.html
Software as an interactive web tool to compare two or more groups of samples in a Gene Expression Omnibus (GEO) series regardless of data type and quality. Used to identify genes that are differentially expressed across experimental conditions. Results are presented as a table of genes ordered by significance.
Proper citation: GEO2R (RRID:SCR_016569) Copy
Web application for integrated analysis and interactive visualization of RNA interference (RNAi) screening data.
Proper citation: CARD (RRID:SCR_016602) Copy
https://github.com/xia-lab/MetaboAnalystR
Software R package for comprehensive analysis of metabolomics data. Contains the R functions and libraries underlying MetaboAnalyst web server, including functions for metabolomic data analysis, visualization, and functional interpretation.
Proper citation: MetaboAnalystR (RRID:SCR_016723) Copy
Software tools for compound-centric data mining and navigation. Used to identify compounds in overlapping and co-eluting peaks with feature extraction and correlation algorithms for chromatographic separation. Used for separating true signals from noise.
Proper citation: Agilent MassHunter WorkStation - Qualitative Analysis for GC/MS (RRID:SCR_016657) Copy
https://visrsoftware.github.io/
Software as an R-based visual framework for analysis of sequencing datasets. Provides a framework for integrative and interactive analyses.
Proper citation: VisR (RRID:SCR_016658) Copy
https://software.broadinstitute.org/gatk/
THIS RESOURCE IS NO LONGER IN SERVICE. Documented on July 18th,2023. Software package for genome analysis. Used for analysis of next generation genomic data in cancer.
Proper citation: IndelGenotyper (RRID:SCR_016663) Copy
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