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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/rizkg/BBHash
Software library for building minimal perfect hash function. Designed to handle large scale datasets.
Proper citation: BBHash (RRID:SCR_023972) Copy
Software DICOM library which provides user-friendly C++11 and Python API for different parts of the DICOM standard.
Proper citation: Odil (RRID:SCR_024140) Copy
Software Python library for phylogenetic computing. Provides classes and functions for simulation, processing, and manipulation of phylogenetic trees and character matrices, and supports the reading and writing of phylogenetic data in range of formats, such as NEXUS, NEWICK, NeXML, Phylip, FASTA., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.
Proper citation: DendroPy (RRID:SCR_024197) Copy
https://github.com/y-256/libdivsufsort
Software library that implements lightweight suffix array construction algorithm. Provides C API to construct suffix array and Burrows-Wheeler transformed string from given string over constant size alphabet. The algorithm runs in O(n log n) worst-case time using only 5n+O(1) bytes of memory space, where n is the length of the string.
Proper citation: libdivsufsort (RRID:SCR_024079) Copy
https://github.com/lh3/miniasm
Software OLC-based de novo assembler for noisy long reads.
Proper citation: Miniasm (RRID:SCR_024114) Copy
https://github.com/cogent3/cogent3
Software Python library for analysis of genomic sequence data. Framework for novel probabilistic analyses of biological sequences, devising workflows, and generating publication quality graphics.
Proper citation: PyCogent (RRID:SCR_024192) Copy
http://libdisorder.freshdefense.net/
Software C library for entropy measurement of byte streams and other data.
Proper citation: libdisorder (RRID:SCR_024072) Copy
https://github.com/open2c/cooler
Software library for sparse, compressed, binary persistent storage format used to store genomic interaction data, such as Hi-C contact matrices.Scalable storage for Hi-C data and other genomically labeled arrays.
Proper citation: Cooler (RRID:SCR_024194) Copy
https://github.com/dib-lab/sourmash
Software library for MinHash sketching of DNAsearch. Used to compare and analyze genomic and metagenomic data sets.
Proper citation: sourmash (RRID:SCR_024347) Copy
Software tool as general purpose cluster algorithm for both weighted and unweighted networks. Unsupervised cluster algorithm for graphs based on simulation of stochastic flow in graphs. Cluster algorithm for graphs.
Proper citation: MCL (RRID:SCR_024109) Copy
https://github.com/BIC-MNI/libminc
Software core library and API of the Medical Image NetCDF toolkit.
Proper citation: libminc (RRID:SCR_024086) Copy
https://github.com/rcsb/mmtf-python
Software Python implementation of MacroMolecular Transmission Format API, decoder and encoder. Repository holds the Python 2 and 3 compatible API, encoding and decoding libraries.
Proper citation: mmtf-python (RRID:SCR_024120) Copy
https://github.com/kdm9/libqcpp
Software C++11 library for next-gen sequence quality control and assessment.
Proper citation: libqc++ (RRID:SCR_024088) Copy
https://github.com/mengyao/Complete-Striped-Smith-Waterman-Library
SIMD Smith-Waterman C/C++ library for use in genomic applications. SSW is a fast implementation of the Smith-Waterman algorithm, which uses the Single-Instruction Multiple-Data (SIMD) instructions to parallelize the algorithm at the instruction level. SSW library provides an API that can be flexibly used by programs written in C, C++ and other languages.
Proper citation: SSW Library (RRID:SCR_024089) Copy
https://svi-opensource.github.io/libics/
Software reference library for Image Cytometry Standard, an open standard for writing images of any dimensionality and data type to file, together with associated information regarding the recording equipment or recorded subject.Image Cytometry Standard file reading and writing.
Proper citation: libics (RRID:SCR_024085) Copy
http://www-personal.umich.edu/~jianghui/rseq/
A software toolkit for RNA sequence data analysis. It contains programs that cover several aspects of RNA-Seq data analysis such as read quality assessment, reference sequence generation, sequence mapping, and gene and isoform expressions estimations.
Proper citation: rSeq (RRID:SCR_000562) Copy
https://services.healthtech.dtu.dk/services/DictyOGlyc-1.1/
Server that produces neural network predictions for GlcNAc O-glycosylation sites in Dictyostelium discoideum proteins.
Proper citation: DictyOGlyc (RRID:SCR_001600) Copy
http://www.glycosciences.de/modeling/glyprot/
Web-based tool that enables meaningful N-glycan conformations to be attached to all the spatially accessible potential N-glycosylation sites of a known three-dimensional (3D) protein structure. The 3D structure of protein is required as input. Potential N-glysylations site are automatically detected. The attached glycan are constructed with SWEET-II, http://www.glycosciences.de/modeling/sweet2/doc/index.php
Proper citation: GlyProt (RRID:SCR_001560) Copy
Database of experimentally verified phosphorylation sites in eukaryotic proteins. Entries are manually curated with links to literature references, information about structure, interaction partners and sub-cellular compartment tissues, and sequences from the UniProt database.
Proper citation: Phospho.ELM (RRID:SCR_001109) Copy
http://hipipe.ncgm.sinica.edu.tw/
Tool that provides high performance NGS (next-generation sequencing) data analysis pipelines so that researchers with minimum IT or bioinformatics knowledge can perform common analyses on NGS data. 3 TB of storage space is reserved for each task.
Proper citation: HiPipe (RRID:SCR_001215) Copy
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