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http://www.technicalreports.org/trail/search/

Repository of technical reports from US government. Identifies, acquires, catalogs, digitizes and provides unrestricted access to U.S. government agency technical reports. Ensures preservation, discoverability, and persistent open access to government technical publications regardless of form or format. Search interface is hosted by University of Washington and searches all TRAIL content found at HathiTrust and UNT.

Proper citation: Trail Technical Report Archive (RRID:SCR_017324) Copy   

•   Source: SciCrunch Registry

https://rdrr.io/cran/WGCNA/man/BrainRegionMarkers.html

Software R package provides matrix of predefined set of marker genes for many regions of the human brain, using data from the Allen Human Brain Atlas.

Proper citation: BrainRegionMarkers (RRID:SCR_023836) Copy   

•   Source: SciCrunch Registry

https://ualr.edu/bioinformatics/midsouth-bioinformatics-center/

Core provides bioinformatics consulting, training, technical assistance, and access to computational infrastructure for faculty, students, and researchers in region with their bioscience computational needs. Offers private sessions, workshops and training on specialty topics. Computing resources including software, computing cluster, technical advice.

Proper citation: University of Arkansas at Little Rock MidSouth Bioinformatics Center Core Facility (RRID:SCR_017168) Copy   

•   Source: SciCrunch Registry

https://github.com/benfulcher/GCEA_FalsePositives

Software toolbox for gene category enrichment analysis false positives available. Used for analysis of statistical biases in Gene Set Enrichment Analysis applied to transcriptomic atlas data.

Proper citation: GCEA_FalsePositives (RRID:SCR_023835) Copy   

•   Source: SciCrunch Registry

https://www.hmtvar.uniba.it

Manually curated database offering variability and pathogenicity information about mtDNA variants. Human mitochondrial variants data of healthy and diseased subjects.Data and text mining pipeline to annotate human mitochondrial variants with functional and clinical information.

Proper citation: HmtVar (RRID:SCR_017288) Copy   

•   Source: SciCrunch Registry

https://github.com/LeonDLotter/ABAnnotate/tree/v0.1.0

Software toolbox for ensemble-based multimodal gene-category enrichment analysis of human neuroimaging data.Performs ensemble-based gene-category enrichment analysis on volumetric human neuroimaging data via brain-wide gene expression patterns derived from Allen Human Brain Atlas. Utilizes nonparametric method using spatial autocorrelation-corrected phenotype null maps for estimation of gene-category null ensembles.

Proper citation: ABAnnotate (RRID:SCR_023833) Copy   

•   Source: SciCrunch Registry

http://s-quest.bihealth.org/fiddle/

Software interactive tool to help researchers to identify most appropriate publication format for their dataset that may be hard to publish in traditional journals. Formats include data repositories, micropublications, preprints, data journals, publishing platforms and journals that are open to null results. Users can search for publication format that meets their needs, compare and contrast formats, and find links to publishers. Open source tool to combat publication bias by getting research out of file drawer and into scientific community.

Proper citation: fiddle (RRID:SCR_017327) Copy   

•   Source: SciCrunch Registry

https://git.io/vAeKZ

It is non-graphical user interface in MATLAB which relies on keyboard callback functions. Used for analyzing big data sets.

Proper citation: ROIs selection with a non-graphical user interface (RRID:SCR_016352) Copy   

•   Source: SciCrunch Registry

https://github.com/BlueBrain/atlas-densities

Software tools to compute densities in context of brain atlases. Used to create BBP Cell Atlas, using Allen Mouse Brain Atlas and collected literature density values.Provides list of volumetric files that provides cell type density estimates for each voxel of mouse brain volume.

Proper citation: Atlas Densities (RRID:SCR_023839) Copy   

•   Source: SciCrunch Registry

https://figshare.com/articles/phi_toolbox_zip/3203326

Toolkit of MATLAB functions for computing integrated information ('phi' or 'Φ') from neural data. The toolbox consists of downloadable codes that perform practical computation.

Proper citation: Phi Toolbox (RRID:SCR_015549) Copy   

•   Source: SciCrunch Registry

http://www.humphreyslab.com/SingleCell/

Software tool as analyzer for kidney single cell datasets. Allows users to query gene expression from mouse or human kidney and human kidney organoid single cell datasets. For details about datasets visit ReBuilding a Kidney website.

Proper citation: Kidney Interactive Transcriptomics (RRID:SCR_017209) Copy   

•   Source: SciCrunch Registry

http://bioconductor.org/packages/EGSEA/

Method developed for RNA-sequencing data. EGSEA combines results from twelve algorithms and calculates collective gene set scores to improve the biological relevance of the highest ranked gene sets.

Proper citation: EGSEA (RRID:SCR_015036) Copy   

•   Source: SciCrunch Registry

https://github.com/BlueBrain/atlas-alignment-meter

Software Python CLI and library to measure jaggyness of brain parcellation volume. Used to measure slice-to-slice jaggedness of volumetric dataset, only in form of NRRD file.

Proper citation: Atlas Alignment Meter (RRID:SCR_023843) Copy   

•   Source: SciCrunch Registry

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

http://emboss.sourceforge.net/apps/cvs/embassy/index.html#DOMSEARCH

Source code for EMBOSS commands to search for protein domains. Its functions include removing redundant and fragment sequences from DHF files, generating PSI-BLAST hits (DHF file) from a DAF file, removing ambiguous classified sequences from DHF files, and generating DHF files from keyword search of UniProt.

Proper citation: Embassy-domsearch (RRID:SCR_016086) Copy   

•   Source: SciCrunch Registry

https://www.rapidnovor.com/resources/wild/

Service that distinguishes Isoleucine and Leucine using mass spectrometry experiments.

Proper citation: WILD (RRID:SCR_016240) Copy   

•   Source: SciCrunch Registry

https://www.nceas.ucsb.edu/

Synthesis science center to help to transform ecology and environmental science to generate bigger insights. Leader in environmental data science, has led development of technological solutions to improve data access and management and efficiency of analyses, and helped set scientific standards in data ethics.

Proper citation: National Center for Ecological Analysis and Synthesis (RRID:SCR_024597) Copy   

•   Source: SciCrunch Registry

https://github.com/CraigList056/iqas

Modeling document labels using Latent Dirichlet Allocation is component tool under Integrated Quality Assurance System of Camarines Sur Polytechnic Colleges which categorizes text of particular document and use it for auto-tagging.

Proper citation: IQAS (RRID:SCR_023146) Copy   

•   Source: SciCrunch Registry

https://searchbreast.org/

Database and repository of tissues relating to mouse models of breast cancer. Users can search and share models, and members can enter details of available material to share on a collaborative basis.

Proper citation: SEARCHBreast (RRID:SCR_014826) Copy   

•   Source: SciCrunch Registry

https://github.com/LearningLocker/learninglocker

Open source software Learning Record Store implementing the xAPI (Tin Can API) e-learning standard.Type of data repository designed to store learning activity statements generated by xAPI (Tin Can) compliant learning activities.

Proper citation: Learning Locker (RRID:SCR_024401) Copy   

•   Source: SciCrunch Registry