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https://www.genome.jp/kegg/pathway.html

Reference database for pathway mapping in KEGG Mapper. Collection of manually drawn pathway maps representing knowledge on molecular interaction, reaction and relation networks for metabolism, genetic information processing, environmental information processing, cellular processes, organisms systems, human diseases, drug development.

Proper citation: KEGG PATHWAY Database (RRID:SCR_018145) Copy   

•   Source: SciCrunch Registry

https://www.cellphonedb.org/

Collection of publicly available data of curated receptors, ligands and their interactions. Integrates existing datasets that pertain to cellular communication and new manually reviewed information. Used to search for particular ligand or receptor or to interrogate single cell transcriptomics data.

Proper citation: CellPhoneDB (RRID:SCR_017054) Copy   

•   Source: SciCrunch Registry

https://dhs.ccm.sickkids.ca/

Collection of open chromatin regions from sequencing data. Metadata as entire curated DNase-I hypersensitive sites (DHS) on the whole genome datasets and data specific to each chromosome.

Proper citation: Database of Open Chromatin Regions (RRID:SCR_016614) Copy   

•   Source: SciCrunch Registry

http://omicslab.genetics.ac.cn/dred/index.php

Database of genes related to Repeat Expansion Diseases, as comprehensive manually curated database that covers all reported repeat expansion diseases included in PubMed and OMIM. Detailed information about each repeat and its related genes/diseases can be found in database, links to OMIM, NCBI and Ensembl are also provided. Provides list of predicted genes containing unstable tandem repeats that may cause diseases via abnormal repeat expansion by support vector machine and random forest.

Proper citation: Database of genes related to Repeat Expansion Diseases (RRID:SCR_018086) Copy   

•   Source: SciCrunch Registry

http://www.mqtldb.org/

Data collection of large scale genome wide DNA methylation analysis of 1,000 mother-child pairs at serial time points across life course (ARIES).

Proper citation: mqtldb (RRID:SCR_018002) Copy   

•   Source: SciCrunch Registry

https://www.postgresql.org/

Open source object relational database system that uses and extends SQL language combined with many features that safely store and scale the most complicated data workloads. PostgreSQL runs on all major operating systems.

Proper citation: PostgreSQL (RRID:SCR_021067) Copy   

•   Source: SciCrunch Registry

https://www.scopus.com/

Abstract and indexing database with full text links that is produced by Elsevier Co. Combines expertly curated abstract and citation database with enriched data and linked scholarly literature across wide variety of disciplines.

Proper citation: Scopus (RRID:SCR_022559) Copy   

•   Source: SciCrunch Registry

https://github.com/clinwiki-org/clinwiki

Clinical trials database.

Proper citation: ClinWiki (RRID:SCR_021297) Copy   

•   Source: SciCrunch Registry

https://trinetx.com/

Network of healthcare organizations, together with data partners in Brazil, South Korea, and Japan, to bring clinical facts on more than 250 million patients around the world. Federated model so users of this data are ensured new patients, observations, and results every day, all harmonized to standard terminology like ICD-10 and LOINC without any data wrangling required at the point of care. The raw data is not available to authors of papers and papers in medicine are being retracted.

Proper citation: trinetx (RRID:SCR_022760) Copy   

•   Source: SciCrunch Registry

http://www.clcbio.com/products/clc-main-workbench/

A suite of software for DNA, RNA and protein sequence data analysis. The software allows for the analysis and visualization of Sanger sequencing data as well as gene expression analysis, molecular cloning, primer design, phylogenetic analyses, and sequence data management.

Proper citation: CLC Main Workbench (RRID:SCR_000354) Copy   

•   Source: SciCrunch Registry

http://www.cs.cmu.edu/~schneide/tut5/node42.html

A model evaluation method for training someone to read data. There are three methods: the holdout method, K-fold cross validation, and leave-one-out cross validation.

Proper citation: Cross Validation (RRID:SCR_000702) Copy   

•   Source: SciCrunch Registry

http://www.bioconductor.org/

Software repository for R packages related to analysis and comprehension of high throughput genomic data. Uses separate set of commands for installation of packages. Software project based on R programming language that provides tools for analysis and comprehension of high throughput genomic data.

Proper citation: Bioconductor (RRID:SCR_006442) Copy   

•   Source: SciCrunch Registry

https://github.com/EpistasisLab/ReBATE

Open source software Python package to compare relief based feature selection algorithms used in data mining. Used for feature selection in any bioinformatics problem with potentially predictive features and target outcome variable, to detect feature interactions without examination of all feature combinations, to detect features involved in heterogeneous patterns of association such as genetic heterogeneity .

Proper citation: ReBATE (RRID:SCR_017139) Copy   

•   Source: SciCrunch Registry

https://www.thermofisher.com/order/catalog/product/CHROMELEON7

Software system to support chromatography operations, to ensure data quality and manage all the analytical processes from instrument control, to raw data storage and processing, through to generating the final results.

Proper citation: Chromeleon Chromatography Data System (CDS) Software (RRID:SCR_016874) Copy   

•   Source: SciCrunch Registry

https://github.com/dorianps/LESYMAP

Software R package to conduct lesion-to-symptom mapping from human MRI data.Takes lesion maps and cognitive performance scores from patients with stroke, and maps brain areas responsible for cognitive deficit.

Proper citation: LESYMAP (RRID:SCR_017967) Copy   

•   Source: SciCrunch Registry

http://download.ant-neuro.com/matlab/

Software as an EEGLAB tool used for LIBEEP recordings.

Proper citation: Libeep EEGLAB plugin (RRID:SCR_016334) Copy   

•   Source: SciCrunch Registry

https://github.com/pachterlab/kb_python

Software Python package that wraps kallisto and bustools single-cell RNA-seq workflow. Used for single-cell RNA-seq pre-processing. Simplifies downloading and running of kallisto and bustools programs. Consists of kb ref and kb count commands. kb ref builds or downloads species specific index for pseudo alignment of reads and must be run prior to kb count and it runs kallisto index. kb count runs kallisto and bustools programs and is used for pre-processing of data from variety of single-cell RNA-seq technologies, and for number of different workflows (e.g. production of gene count matrices, RNA velocity analyses, etc.).

Proper citation: kb_python (RRID:SCR_018213) Copy   

•   Source: SciCrunch Registry

http://noble.gs.washington.edu/proj/genomedata/

A format for efficient storage of multiple tracks of numeric data anchored to a genome. The format allows fast random access to hundreds of gigabytes of data, while retaining a small disk space footprint. They have also developed utilities to load data into this format. Retrieving data from this format is more than 2900 times faster than a naive approach using wiggle files. A reference implementation in Python and C components is available here under the GNU General Public License. The software has only been tested on Linux and Mac systems.

Proper citation: Genomedata (RRID:SCR_004544) Copy   

•   Source: SciCrunch Registry

http://harvard.eagle-i.net/i/0000012a-2518-fb6c-5617-794280000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core provides services: RT PCR service, Gene expression profiling service, Proteomics analysis service, Bioinformatics and Systems Biology analyses, Next Generation Sequencing Service, Affymetrix Human and Mouse Gene 2.0 ST Arrays and 2.1 ST Arrayplates. Core proteomics facility for the Dana-Farber/Harvard Cancer Center. Workflows and algorithms for analysis of next-generation sequencing data including RNA-Seq, ChIP-Seq, Epigenetics-Seq and DNA seq, Comprehensive workflow for analysis of Microbiome sequencing data, Integrated systems biology analysis of transcriptome, miRNA, epigenome, metabolomics and proteomics data. Pipelines: MALDI Tissue imaging and targeted quantitative proteomics.

Proper citation: Beth Israel Deaconess Medical Center Genomics Proteomics Bioinformatics and Systems Biology Center (RRID:SCR_009668) Copy   

•   Source: SciCrunch Registry

http://montana.eagle-i.net/i/0000012b-00be-4e65-df3b-3fdc80000000

THIS RESOURCE IS NO LONGER IN SERVICE. Documented on October 27, 2023. Core for Microarray analysis, Database development, Systems biology analysis, Genome assembly, Pathway data analysis, Expression data analysis, Metagenomics analysis. To maintain equipment and software for bioinformatic research, promote bioinformatics education on the MSU campus, and provide training and support to biologists implementing bioinformatics tools in their research.

Proper citation: Montana State University Bioinformatics Core Facility (RRID:SCR_009937) Copy   

•   Source: SciCrunch Registry