Tools   Select Another Resource Report Type

https://github.com/jkrijthe/Rtsne

Software as R wrapper for Van der Maaten's Barnes-Hut implementation of t-Distributed Stochastic Neighbor Embedding. Used for high-dimentional data visualisation.

Proper citation: Rtsne (RRID:SCR_016342) Copy   

•   Source: SciCrunch Registry
  

https://amp.pharm.mssm.edu/biojupies/

Software as an open source web server that automatically generates RNA-seq data analysis of jupyter notebooks. It allows creation and containment of documents that have live code, visualizations and narrative text.

Proper citation: BioJupies (RRID:SCR_016346) Copy   

•   Source: SciCrunch Registry
  

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

Software as an open source package for assessing transcriptional changes and characterizing heterogeneity in single-cell RNA sequencing data.

Proper citation: MAST (RRID:SCR_016340) Copy   

•   Source: SciCrunch Registry
  

https://www.ebi.ac.uk/metagenomics/

Portal for the analysis and exploration of metagenomic, metatranscriptomic, amplicon and assembly data. Provides functional and taxonomic analyses of user-submitted sequences, as well as analysis of publicly available metagenomic datasets held within the European Nucleotide Archive (ENA).Microbiome analysis resource in 2020.

Proper citation: MGnify (RRID:SCR_016429) Copy   

•   Source: SciCrunch Registry
  

http://viewtool.chenglab.com/

Web application viewer for large microscopy data.

Proper citation: ViewTool Cheng Lab (RRID:SCR_016430) Copy   

•   Source: SciCrunch Registry
  

https://www.t2depigenome.org/

Collects and provides data on the human genome and epigenome to facilitate genetic studies of type 2 diabetes and its complications. A component of the AMP T2D consortium, which includes the National Institute for Diabetes and Digestive and Kidney Diseases (NIDDK) and an international collaboration of researchers.

Proper citation: Diabetes Epigenome Atlas (RRID:SCR_016441) Copy   

•   Source: SciCrunch Registry
  

https://www.myassays.com/

Software tool for assay data analysis.

Proper citation: MyAssays (RRID:SCR_016562) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

http://www.actigraphy.com/solutions/actiware/

Software package to analyze, manage, and export recorded activity data from all Actiwatch models. Used to view long-term sleep/wake patterns, activity, illuminance, and event markers in an easy-to-read actogram format.

Proper citation: Respironics Actiware (RRID:SCR_016440) Copy   

•   Source: SciCrunch Registry
  

http://bioinfogp.cnb.csic.es/tools/venny/

Software tool for comparing lists with Venn's diagrams.

Proper citation: Venny 2.1 (RRID:SCR_016561) Copy   

•   Source: SciCrunch Registry
  

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://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://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
  

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
  

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   

•   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