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SciCrunch Registry is a curated repository of scientific resources, with a focus on biomedical resources, including tools, databases, and core facilities - visit SciCrunch to register your resource.
https://github.com/ekg/fastahack
Software application for indexing and extracting sequences and subsequences from FASTA files. It will only generate indexes for FASTA files in which the sequences have self-consistent line lengths.
Proper citation: Fastahack (RRID:SCR_016090) Copy
https://github.com/HMPNK/CSA2.6
Software pipeline for high-throughput chromosome level vertebrate genome assembly. Pipeline, which after contig assembly performs post assembly improvements by ordering assembly and closing gaps, as well as splitting of low supported regions.
Proper citation: Chromosome Scale Assembler (RRID:SCR_017960) Copy
https://github.com/dmis-lab/biobert
Pre-trained biomedical language representation model for biomedical text mining. This repository provides fine-tuning codes of BioBERT, language representation model for biomedical domain, especially designed for biomedical text mining tasks such as biomedical named entity recognition, relation extraction, question answering, etc.
Proper citation: BioBERT (RRID:SCR_017547) Copy
https://github.com/OpenMendel/MendelIHT.jl
Software Julia package that implements iterative hard thresholding as multiple regression model for GWAS. Built-in support for handling PLINK and VCF files, parallel computing, fits a variety of GLM models, and handles grouping/weighting SNPs.
Proper citation: MendelIHT.jl (RRID:SCR_018292) Copy
Software distribution management for life sciences. Channel for Conda package manager specializing in bioinformatics software. Consists of repository of recipes hosted on GitHub, build system turning these recipes into conda packages, repository of packages containing bioinformatics packages ready to use with conda install.
Proper citation: BioConda (RRID:SCR_018316) Copy
https://github.com/mridulaprasad/CorrDrugTumorMSI
Software R pipeline to correlate drug distribution with tumor tissue types in mass spectrometry imaging data.
Proper citation: CorrDrugTumorMSI (RRID:SCR_018962) Copy
https://github.com/cobilab/geco3/
Software tool as DNA compressor that uses neural network to do mixing of experts.
Proper citation: GeCo3 (RRID:SCR_018877) Copy
https://github.com/liqiwei2000/BayesEpiModels
Software tool for accessing performance of different epidemiological models, including both growth and compartmental models, in Bayesian framework.
Proper citation: BayesEpiModels (RRID:SCR_019291) Copy
https://metacpan.org/dist/Bio-Chado-Schema
Standard object-relational mapping layer for use with GMOD Chado database schema. This layer is implemented with DBIx::Class, generated with the help of DBIx::Class::Schema::Loader module.
Proper citation: Bio-Chado-Schema (RRID:SCR_024059) Copy
Open source Python-based optimization modeling language with diverse set of optimization capabilities.
Proper citation: pyomo (RRID:SCR_024188) Copy
https://metacpan.org/dist/AI-FANN
Software Perl wrapper for the Fast Artificial Neural Network library
Proper citation: AI-FANN (RRID:SCR_024060) Copy
https://metacpan.org/dist/Bio-Coordinate
Software application used for working with various biological coordinate systems. See Bio::Coordinate::Collection and Bio::Collection::Pair for examples.
Proper citation: Bio-Coordinate (RRID:SCR_024063) Copy
Software advanced DICOM viewer and dicomizer that can also be used to convert png, jpeg, bmp, pdf, tiff to DICOM files.
Proper citation: Ginkgo CADx (RRID:SCR_024031) Copy
http://samtools.github.io/htsjdk/
Software implementation of unified Java library for accessing common file formats, such as SAM and VCF, used for high-throughput sequencing data. There are also an number of useful utilities for manipulating HTS data.
Proper citation: HTSJDK (RRID:SCR_024036) Copy
http://proteomics.ucsd.edu/Software/Inspect/
Software tool to addresses several algorithmic problems in order to identify modified proteins.Software MS/MS database search tool specifically designed to address two crucial needs of the proteomics comminuty: post-translational modification identification and search speed.
Proper citation: InsPecT (RRID:SCR_024038) Copy
http://bibus-biblio.sourceforge.net/
Bibliographic and reference management software. Allows to search, edit, and sort bibliographic records.
Proper citation: Bibus (RRID:SCR_023974) Copy
https://github.com/klebgenomics/Kaptive
Software tool to report information about surface polysaccharide loci for Klebsiella pneumoniae species complex and Acinetobacter baumannii genome assemblies.
Proper citation: Kaptive (RRID:SCR_024046) Copy
Open source, software cross platform citation and reference management tool.Helps to collect and organize sources, find the paper, discover the latest research.
Proper citation: JabRef (RRID:SCR_024047) Copy
https://userbase.kde.org/KBibTeX
Software tool as bibliography editor for KDE. Used in conjunction with Kile. BibTeX editor for KDE. KBibTeX's primary file format is BibTeX as known from LaTeX, but other formats such as RIS, PDF, or RTF can be imported and exported.
Proper citation: KBibTeX (RRID:SCR_024048) Copy
https://github.com/kblin/ncbi-acc-download
Software tool as partner script to the popular ncbi-genome-download script. Allows to download sequences from GenBank/RefSeq by accession through the NCBI ENTREZ API.
Proper citation: NCBI accession download script (RRID:SCR_024130) Copy
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