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on page 1 showing 19 out of 19 results

    AFIDs

Cite this (AFIDs, RRID:SCR_016623)

URL: https://github.com/jclauneuro/afids

Resource Type: Resource, software resource, software application, image processing software, data processing software, software toolkit

Software tool as an open framework for evaluating correspondence between magnetic resonance images of the human brain using fiducial placement.

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Cite this (brainlife.io, RRID:SCR_016513)

URL: http://www.nitrc.org/projects/brainlife_io/

Resource Type: Resource, portal, data or information resource

Platform for publishing reproducible code and datasets and providing access to national supercomputers, private clouds, and institutional high-performance computer systems to promote open software and data sharing to advance understanding of the human brain.

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    BWA

Cite this (BWA, RRID:SCR_010910)

URL: http://bio-bwa.sourceforge.net/

Resource Type: Resource, image analysis software, data analysis software, data processing software, alignment software, software application, sequence analysis software, software resource

Software for aligning sequencing reads against large reference genome. Consists of three algorithms: one for sequence reads up to 100bp, and other two for longer sequences ranged from 70bp to 1Mbp.

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Cite this (Connectome Computation System, RRID:SCR_017342)

URL: https://github.com/zuoxinian/CCS

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software tool for multimodal human brain imaging data analysis. Computational pipeline for discovery science of human brain connectomes at macroscale with multimodal magnetic resonance imaging technologies.

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Cite this (Discovar assembler, RRID:SCR_016755)

URL: https://software.broadinstitute.org/software/discovar/blog/

Resource Type: Resource, software resource, data processing software, data analysis software, sequence analysis software, software application

Software tool for variant calling with reference and de novo assembly of genomes. The heart of DISCOVAR is a de novo genome assembler which can generate de novo assemblies for both large and small genomes.

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Cite this (EpiFactors , RRID:SCR_016956)

URL: http://epifactors.autosome.ru/

Resource Type: Resource, data or information resource, database

Manually curated collection of human epigenetic factors, their complexes, corresponding genes and products.

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    GEMINI

Cite this (GEMINI, RRID:SCR_014819)

URL: https://gemini.readthedocs.io/en/latest/

Resource Type: Resource, software resource

Framework for exploring genetic variation in the context of the genome annotations available for the human genome. Users can load a VCF file into a database and each variant is automatically annotated by comparing it to several genome annotations from source such as ENCODE tracks, UCSC tracks, OMIM, dbSNP, KEGG, and HPRD.

  • From Current Category

Cite this (Human Microbiome Project, RRID:SCR_012956)

URL: https://commonfund.nih.gov/hmp/

Resource Type: Resource, organization portal, data analysis software, data processing software, software application, service resource, portal, storage service resource, software resource, data repository, data or information resource

NIH Project to generate resources to characterize the human microbiota and to analyze its role in human health and disease at several different sites on the human body, including nasal passages, oral cavities, skin, gastrointestinal tract, and urogenital tract using metagenomic and traditional approach to genomic DNA sequencing studies.

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Cite this (JOINSOLVER, RRID:SCR_016619)

URL: https://joinsolver.niaid.nih.gov

Resource Type: Resource, image analysis software, data analysis software, data processing software, alignment software, software application, service resource, software resource

Software tool to analyze human immunoglobulin V(D)J recombination and performing Ig nucleotide and amino acid alignment, as well as extensive mutation and Complementarity Determining Region 3 (CDR3H) analysis.

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Cite this (Kidney Interactive Transcriptomics, RRID:SCR_017209)

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

Resource Type: Resource, analysis service resource, service resource, data or information resource, production service resource

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.

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    LungMap

Cite this (LungMap, RRID:SCR_016347)

URL: https://www.lungmap.net/

Resource Type: Resource, service resource, portal, data repository, storage service resource, data or information resource

Portal for lung histochemistry data. For structural and molecular data regarding normal perinatal and postnatal lung development in the mouse and human. For public sharing of data sets, establishing a repository of young human lung tissues obtained through organ donor organizations, and developing a comprehensive lung ontology .Contains lung images and transcriptomic, proteomic, and lipidomic human and mouse data and provides scientific information to stimulate interest in research careers. Used to serve as a research resource and public education tool.

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Cite this ( Metscape , RRID:SCR_014687)

URL: http://metscape.ncibi.org

Resource Type: Resource, software resource, source code, resource

A software program that allows users to visualize and interpret human metabolim and expression profiling data by providing users with a bioinformatics framework. Its features include bulding and analyzing networks of genes and compounds, identifying enriched pathways from expression profiling data, and visualizing changes in metabolite data.

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    mirDIP

Cite this (mirDIP, RRID:SCR_016770)

URL: http://ophid.utoronto.ca/mirDIP/

Resource Type: Resource, data or information resource, portal, database

microRNA data integration portal to find microRNAs that target a gene, or genes targeted by a microRNA, in Homo sapiens. Software to integrate prediction databases to elucidate accurate microRNA:target relationships. Used for human microRNA prediction studies.

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Cite this (PathwayNet, RRID:SCR_017353)

URL: http://pathwaynet.princeton.edu/

Resource Type: Resource, data analysis service, data access protocol, production service resource, analysis service resource, web service, service resource, software resource

Web user interface for interaction predictions of human gene networks and integrative analysis of user data types that takes advantage of data from diverse tissue and cell-lineage origins. Predicts presence of functional association and interaction type among human genes or its protein products on whole genome scale. Used to analyze experimetnal gene in context of interaction networks.

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    PhenoSpD

Cite this (PhenoSpD, RRID:SCR_016359)

URL: https://github.com/MRCIEU/PhenoSpD

Resource Type: Resource, software resource, software application, data analysis software, data processing software, software toolkit

Software toolkit for phenotypic correlation estimation and multiple testing correction (Spectral Decomposition, SpD) for human phenome using genome-wide association study (GWAS) summary statistics. It is a command line R based tool.

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    PyMINEr

Cite this (PyMINEr, RRID:SCR_016990)

URL: https://www.sciencescott.com/pyminer

Resource Type: Resource, software resource, software application, data analysis software, data processing software

Software tool to automate cell type identification, cell type-specific pathway analyses, graph theory-based analysis of gene regulation, and detection of autocrine-paracrine signaling networks. Finds Gene and Autocrine-Paracrine Networks from Human Islet scRNA-Seq.

  • From Current Category

Cite this (Seek & blastn, RRID:SCR_016625)

URL: http://scigendetection.imag.fr/TPD52/

Resource Type: Resource, data analysis service, data analysis software, data processing software, production service resource, analysis service resource, software application, sequence analysis software, service resource, software resource

Software semiautomated application as a text mining and text analysis tool to search and extract gene identifiers and nucleotide sequences against the human genomic and transcript database. Seeks for nucleotide sequences in pdf files and then call a local version of blastn.

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    SNP2TFBS

Cite this (SNP2TFBS, RRID:SCR_016885)

URL: http://ccg.vital-it.ch/snp2tfbs

Resource Type: Resource, web service, software resource, data or information resource, data access protocol, database

Collection of text files providing specific annotations for human single nucleotide polymorphisms (SNPs), namely whether they are predicted to abolish, create or change the affinity of one or several transcription factor (TF) binding sites. Used to investigate the molecular mechanisms underlying regulatory variation in the human genome. SNP2TFBS is also accessible over a web interface, enabling users to view the information provided for an individual SNP, to extract SNPs based on various search criteria, to annotate uploaded sets of SNPs or to display statistics about the frequencies of binding sites affected by selected SNPs.

  • From Current Category

Cite this (The 10000 Immunomes, RRID:SCR_016624)

URL: http://10kimmunomes.org

Resource Type: Resource, data or information resource, database

Collection of reference datasets for human immunology, derived from control subjects in the NIAID ImmPort database . Available data include flow cytometry, CyTOF, multiplex ELISA, gene expression, HAI titers, clinical lab tests, HLA type, and others.

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