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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/voutcn/megahit
Software tool as Next Generation Sequencing assembler. Optimized for metagenomes, but also works well on generic single genome assembly (small or mammalian size) and single cell assembly. Can assemble genome sequences from metagenomic datasets of hundreds of Giga base-pairs in time and memory efficient manner on single server.
Proper citation: MEGAHIT (RRID:SCR_018551) Copy
http://ccb.jhu.edu/software/stringtie/gff.shtml
Open source software tool to manipulate files in GFF format. Used to convert, sort, filter, transform, or cluster genomic features.
Proper citation: gffread (RRID:SCR_018965) Copy
https://github.com/nanoporetech/pychopper
Software tool to identify, orient and trim full length Nanopore cDNA reads. Able to rescue fused reads.
Proper citation: Pychopper (RRID:SCR_018966) Copy
https://github.com/BGI-Qingdao/TGS-GapCloser
Software tool that uses long reads to enhance genome assembly. Fast and accurate gap closing software tool that uses low coverage of error-prone long reads generated by third generation sequence techniques (Pacbio, Oxford Nanopore, etc.) or preassembled contigs for large genomes.
Proper citation: TGS-GapCloser (RRID:SCR_017633) Copy
https://github.com/brentp/mosdepth
Software command line tool for rapidly calculating genome wide sequencing coverage. Measures depth from BAM or CRAM files at either each nucleotide position in genome or for sets of genomic regions. Used for fast BAM/CRAM depth calculation for WGS, exome, or targeted sequencing quick coverage calculation for genomes and exomes.
Proper citation: mosdepth (RRID:SCR_018929) Copy
https://github.com/AnacletoLAB/parSMURF
Open source software package as high performance computing imbalance aware machine learning tool for genome wide detection of pathogenic variants.
Proper citation: parSMURF (RRID:SCR_017560) Copy
https://github.com/hms-dbmi/EHRtemporalVariability
Software R package for delineating temporal dataset shifts in electronic health records. Functions to delineate temporal dataset shifts in electronic health records through projection and visualization of dissimilarities among data temporal batches.Enables exploration and identification of dataset shifts, contributing to broadly examine and repurpose large, longitudinal datasets. Used to help ensure reliable data reuse to biomedical data users.
Proper citation: EHRtemporalVariability (RRID:SCR_018663) Copy
https://github.com/nch-igm/rna-stability
Software tool as parallel processing framework for large scale generation of secondary RNA structures and folding statistics for transcriptome of any species.
Proper citation: rna-stability (RRID:SCR_019259) Copy
https://radar-base.org/index.php/home/about-us/
Open source mobile health platform for collecting, monitoring, and analyzing data using sensors, wearables, and mobile devices. Enables study design and set up, active and passive remote data collection, secure data transmission via Wifi and/or Bluetooth and scalable solutions for data storage, management and access. Allows study participants to share their health data with clinicians and researchers in secure way.
Proper citation: RADAR-base (RRID:SCR_019233) Copy
https://github.com/Washington-University/CiftiLib
Software C++ Library for reading and writing CIFTI-2 and CIFTI-1 files.
Proper citation: CiftiLib (RRID:SCR_023996) Copy
https://github.com/rvaser/bioparser/
Software C++ library for parsing several formats in bioinformatics. C++ header only parsing library for several bioinformatics formats (FASTA/Q, MHAP/PAF/SAM), with support for zlib compressed files.
Proper citation: Bioparser (RRID:SCR_024065) Copy
Software memory efficient bioinformatics library written in D programming language whose aim is to provide platform for developing high performance computational biology applications using the D programming language through automatic parallelization of tasks where possible and by avoiding unnecessary memory allocations.
Proper citation: BioD (RRID:SCR_024062) Copy
https://github.com/IRCAD-IHU/camp
Software multi-purpose reflection library developped by Technogerma Systems France and then by Tegesoft. Provides extra layer of flexibility to programs, and allows them to fully expose their data structures at runtime.
Proper citation: CAMP (RRID:SCR_023981) Copy
https://github.com/ggonnella/gfapy
Software library for handling sequence graphs in Python.
Proper citation: GfaPy (RRID:SCR_024030) Copy
Software application as simultaneous Bayesian inference of alignment and phylogeny. Used to estimate multiple sequence alignments and evolutionary trees from DNA, amino acid, or codon sequences. to explore the joint space of alignment and phylogeny given molecular sequence data. BAli-Phy version 3 is model based co-estimation of alignment and phylogeny. Version 3 is substantially faster for large trees, and implements covarion models, additional codon models and other new models. Implements ancestral state reconstruction, allows prior selection for all model parameters, and can also analyze multiple genes simultaneously.
Proper citation: BAli-Phy (RRID:SCR_023976) Copy
https://ismrmrd.github.io/apidocs/1.5.0/
Prerequisite for sharing magnetic resonance imaging reconstruction algorithms and code is a common raw data format. This repository describes such common raw data format, which attempts to capture the data fields that are required to describe the magnetic resonance experiment with enough detail to reconstruct images. The repository also contains a C/C++ library for working with the format.
Proper citation: ISMRMRD (RRID:SCR_024043) Copy
Open Source software modular Java libraries for cheminformatics.
Proper citation: CDK (RRID:SCR_023985) Copy
https://github.com/gramos/imagetooth
Software library to generate images for odontograms.Allows to choose between png or jpg images.
Proper citation: ImageTooth (RRID:SCR_024039) Copy
https://github.com/rdpstaff/TaxonomyTree
Software library used by other RDP tools.TaxonomyTree building and traversal utility classes.
Proper citation: TaxonomyTree (RRID:SCR_024090) Copy
https://metacpan.org/dist/Sort-Key-Top
Functions available from this module select the top n elements from a list using several common orderings and custom key extraction procedures.
Proper citation: Sort-Key-Top (RRID:SCR_024092) Copy
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