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http://www.ngsp.org

Project that aims to standardize Hemoglobin A1c test results to those of the Diabetes Control and Complications Trial (DCCT) and United Kingdom Prospective Diabetes Study (UKPDS) which established the direct relationships between HbA1c levels and outcome risks in patients with diabetes.

Proper citation: National Glycohemoglobin Standardization Program (RRID:SCR_015885) Copy   

•   Source: SciCrunch Registry

https://bitbucket.org/nicofmay/basta-bayesian-structured-coalescent-approximation/src/master/

Software package as Bayesian method to infer migration from genetic data. Implemented in BEAST2 that combines accuracy of methods based on structured coalescent with computational efficiency required to handle more than few populations.

Proper citation: BASTA (RRID:SCR_017303) Copy   

•   Source: SciCrunch Registry

https://geomagic-studio.software.informer.com/12.0/

Software tool to convert 3D scans into parametric models. Transforms 3D scan data into highly accurate surface, polygon and native CAD models. Used for reverse engineering, product design, rapid prototyping and analysis.

Proper citation: GEOMAGIC Studio (RRID:SCR_016978) Copy   

•   Source: SciCrunch Registry

https://github.com/dvera/albacore

Data processing basecaller for the Oxford Nanopore sequencer that identifies DNA sequences directly from raw data. It enhances accuracy of the single-read sequence data, contributing to high consensus accuracy for nanopore sequence data.

Proper citation: Albacore (RRID:SCR_015897) Copy   

•   Source: SciCrunch Registry

https://www.nsrusa.org

Organization that provides instructions for and research on the Natural Stress Relief (NSR) meditation method.

Proper citation: Natural Stress Relief (RRID:SCR_015898) Copy   

•   Source: SciCrunch Registry

https://github.com/eulerlab/QDSpy

Software Python tool for scripting and presenting stimuli for visual neuroscience.

Proper citation: QDSpy (RRID:SCR_016985) Copy   

•   Source: SciCrunch Registry

https://web.stanford.edu/group/pritchardlab/structure.html

Software package for using multi locus genotype data to investigate population structure. Used for inferring presence of distinct populations, assigning individuals to populations, studying hybrid zones, identifying migrants and admixed individuals, and estimating population allele frequencies in situations where many individuals are migrants or admixed. Can be applied to most of commonly used genetic markers, including SNPS, microsatellites, RFLPs and Amplified Fragment Length Polymorphisms.

Proper citation: STRUCTURE (RRID:SCR_017637) Copy   

•   Source: SciCrunch Registry

https://community.brain-map.org/t/allen-human-reference-atlas-3d-2020-new/405

Parcellation of adult human brain in 3D, labeling every voxel with brain structure spanning 141 structures. These parcellations were drawn and adapted from prior 2D version of adult human brain atlas.

Proper citation: Allen Human Reference Atlas, 3D, 2020 (RRID:SCR_017764) Copy   

•   Source: SciCrunch Registry

https://www.gnu.org/software/sed/

Software tool as non interactive command line text editor. Command line that works with streams of characters for searching, filtering and text processing. Used for extracting part of file using pattern matching or substituting multiple occurrences of string within file.

Proper citation: GNU sed (RRID:SCR_018215) Copy   

•   Source: SciCrunch Registry

https://github.com/isovic/racon

Software tool as de novo genome assembly from long uncorrected reads. Used to correct raw contigs generated by rapid assembly methods which do not include consensus step. Supports data produced by Pacific Biosciences and Oxford Nanopore Technologies.

Proper citation: Racon (RRID:SCR_017642) Copy   

•   Source: SciCrunch Registry

https://github.com/Brazelton-Lab/seq-annot

Software Python package for annotating and counting genomic features in genomes and metagenomes. Software tools to facilitate annotation and comparison of genomes and metagenomes.

Proper citation: seq-annot (RRID:SCR_018731) Copy   

•   Source: SciCrunch Registry

https://www.gnu.org/software/grep/manual/grep.html

Software tool to searches one or more input files for lines containing a match to a specified pattern. Prints lines that contain match for one or more patterns. Command-line utility for searching plain-text data sets for lines that match regular expression. When finds match, it copies line to standard output (by default), or produces whatever other sort of output you have requested with options.

Proper citation: GNU Grep (RRID:SCR_018212) Copy   

•   Source: SciCrunch Registry

https://github.com/TransDecoder/TransDecoder

Software tool to identify candidate coding regions within transcript sequences, such as those generated by de novo RNA-Seq transcript assembly using Trinity, or constructed based on RNA-Seq alignments to genome using Tophat and Cufflinks.Starts from FASTA or GFF file. Can scan and retain open reading frames (ORFs) for homology to known proteins by using BlastP or Pfam search and incorporate results into obtained selection. Predictions can then be visualized by using genome browser such as IGV.

Proper citation: TransDecoder (RRID:SCR_017647) Copy   

•   Source: SciCrunch Registry

https://github.com/shendurelab/LACHESIS

Software tool for chromosome scale scaffolding of de novo genome assemblies based on chromatin interactions.Method exploits signal of genomic proximity in Hi-C datasets for ultra long range scaffolding of de novo genome assemblies.

Proper citation: LACHESIS (RRID:SCR_017644) Copy   

•   Source: SciCrunch Registry

https://www.gnu.org/software/tar/

Software tool to create tar archives, as well as various other kinds of manipulation. Used to extract files, to store additional files, or to update or list files which were already stored. Can direct its output to available devices, files, or other programs, can access remote devices or files.

Proper citation: GNU Tar (RRID:SCR_018216) Copy   

•   Source: SciCrunch Registry

https://kona.nhgri.nih.gov/mnemiopsis/

Portal to obtain genomic information on Mnemiopsis. Data available provide annotations and other key biological information not available elsewhere. Used to advance research projects aimed at understanding phylogenetic diversity and evolution of proteins that play fundamental role in metazoan development. Collection of sequenced, assembled, annotated, and performed preliminary analysis of genome of Mnemiopsis.

Proper citation: Mnemiopsis Genome Project Portal (RRID:SCR_018293) Copy   

•   Source: SciCrunch Registry

http://www.twins.org.au/

Portal for Twins Research Australia. Brings twins and researchers together for vital health research in twins.

Proper citation: Twins Research Australia (RRID:SCR_017485) Copy   

•   Source: SciCrunch Registry

https://www.gnu.org/software/gawk/manual/gawk.html

Software tool to select particular records in file and perform operations upon them. awk utility interprets special purpose programming language that makes it possible to handle simple data reformatting jobs with few lines of code. Source code for latest release of GNU awk is available from GNU project ftp server and its many mirrors.

Proper citation: GNU Awk (RRID:SCR_018211) Copy   

•   Source: SciCrunch Registry

https://www.jax.org/news-and-insights/2013/february/komp2-mice-phenotyping-and-availability

Knockout Mouse Phenotyping Project, JAX information about their contributions to KOMP2 project. Project to generate and phenotype single gene KO mouse strains from KOMP ES cell lines. Strains are phenotyped using protocols in pipeline designed by International Mouse Phenotyping Consortium. There are three NIH-funded phenotyping centers in United States: JAX, BaSH Consortium (Baylor College of Medicine, the Wellcome Trust Sanger Institute and MRC Harwell), and the DTCC Consortium (University of California at Davis, the Toronto Center for Phenogenomics, Children’s Hospital Oakland Research Institute (CHORI) and Charles River ).

Proper citation: KOMP2 (RRID:SCR_017528) Copy   

•   Source: SciCrunch Registry

https://www.nitrc.org/search/?type_of_search=group&q=wisconsin&sa.x=0&sa.y=0&sa=Search

Atlases enable alignment of individual scans to improve localization and statistical power of results, and allow comparison of results between studies and institutions. Set of multi subject atlas templates is constructed specifically for functional and structural imaging studies of rhesus macaque.

Proper citation: Rhesus Macaque Brain Atlases (RRID:SCR_017533) Copy   

•   Source: SciCrunch Registry