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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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://bitbucket.org/biobakery/biobakery/wiki/Home

Analysis environment and collection of individual software tools to process raw shotgun metagenome or metatranscriptome sequencing data for quantitative microbial community profiling. Used for a metaomics data analysis., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: biobakery (RRID:SCR_016596) Copy   

•   Source: SciCrunch Registry

https://unpaywall.org/

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   

•   Source: SciCrunch Registry

https://github.com/vaklip/rsfmri_fconn

Software program for preprocessing resting state functional magnetic resonance imaging (rsfMRI) measurements and calculating region of interest based whole brain functional connectivity.

Proper citation: rsfMRI_fconn calculation (RRID:SCR_016591) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/tw/zt/home/life-science/microarray-analysis/microarray-analysis-instruments-software-services/microarray-analysis-software/affymetrix-transcriptome-analysis-console-software.html

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

http://phenomenal-h2020.eu/

Cloud based standardised European e-infrastructure for metabolomics and phenomics data processing, analysis and information mining on public or private cloud providers. Used for large scale computing for medical metabolomics.

Proper citation: PhenoMeNal (RRID:SCR_016605) Copy   

•   Source: SciCrunch Registry

https://niaid.github.io/spice/

Software application for data mining and visualization. Used for analyzes of large FLOWJO data sets from polychromatic flow cytometry and organizing the normalized data graphically.

Proper citation: SPICE (RRID:SCR_016603) Copy   

•   Source: SciCrunch Registry

https://sleepdata.org/

System for sharing sleep data. Organization portal that aggregates, harmonizes, and organizes sleep and clinical data from individuals studied as part of cohort studies or clinical trials and provides suite of tools to facilitate data exploration and data visualization. National Heart, Lung, and Blood Institute resource designed to provide big data resources to sleep research community.

Proper citation: National Sleep Research Resource (NSRR) (RRID:SCR_016576) Copy   

•   Source: SciCrunch Registry

https://github.com/vetscience/Assemblosis

Software tool as a Common Workflow Language (CWL) based automated bioinformatics workflow to assemble haploid/diploid eukaryote genomes of non-model organisms using PacBio long-reads and Illumina short-reads.

Proper citation: Assemblosis (RRID:SCR_016571) Copy   

•   Source: SciCrunch Registry

https://sleepdata.org/datasets/haassa

Portal for sleep-disordered breathing (SDB) in an elderly cohort of Japanese-American men under surveillance for Alzheimer disease (AD) and other dementias. Data to assess relationships between SDB and cognitive performance in late life.

Proper citation: Honolulu-Asia Aging Study of Sleep Apnea (RRID:SCR_016587) Copy   

•   Source: SciCrunch Registry

https://sleepdata.org/datasets/cfs

Portal for family based study of sleep apnea. Contains data for quantifying the familial aggregation of sleep apnea. The polysomnographic (PSG) montage signals: EEG, ECG, EOG, EMG, SpO2, plethysmography, airflow (thermistor), nasal pressure, respiratory effort, position, snore.

Proper citation: Cleveland Family Study (RRID:SCR_016585) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://majiq.biociphers.org/

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   

•   Source: SciCrunch Registry

http://odc-sci.org

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry