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URL: https://bitbucket.org/biobakery/biobakery/wiki/Home
Proper Citation: biobakery (RRID:SCR_016596)
Description: 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.
Synonyms: bioBakery, biobakery
Resource Type: data analysis software, data processing software, software application, software resource, software toolkit
Defining Citation: PMID:29194469
Keywords: Huttenhower lab, metaomics, data, analysis, process, raw, shotgun, metagenome, metatranscriptome, sequencing, microbial, profiling, bio.tools
Funding: ARO W911NF1110473; NHGRI R01 HG005220; NHGRI R01 HG005969; NIDDK U54 DE023798; NSF DBI1053486; Sloan Foundation 4406J0B
Availability: THIS RESOURCE IS NO LONGER IN SERVICE
Resource Name: biobakery
Resource ID: SCR_016596
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Source: SciCrunch Registry (RRID:SCR_005400)
Description: Interactive portal for finding and submitting biomedical resources. Resources within SciCrunch have assigned RRIDs which are used to cite resources in scientific manuscripts. SciCrunch Registry, formerly NIF Registry, provides resources catalog. Allows to add new resources. Allows edit existing resources after registration. Curators are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping contents current.
URL: https://rrid.site/rin/sources/SCR_005400
The data sets included in this resource are published in Kravitz et al, 2012. Distinct roles for direct and indirect pathway striatal neurons in reinforcement (Nat. Neurosci).
