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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
Software package for analyzing, processing and visualizing multi-dimensional microscopy images. Multipurpose postprocessing tool for bioimaging. Can be used for simple visualization of multi-channel temporal image stacks to complex 3D rendering of multiple channels at once.
Proper citation: BioImageXD (RRID:SCR_023979) Copy
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
https://github.com/gt1/bambamc
Software package contains lightweight C implementation of name collating BAM file input and BAM file output.
Proper citation: bambamc (RRID:SCR_023970) Copy
https://github.com/hall-lab/bamkit
Software tools for common BAM file manipulations.
Proper citation: bamkit (RRID:SCR_023969) Copy
https://code.google.com/archive/p/kempbasu/
Software package implements two significance tests for comparing digital gene expression profiles. They provide two programs: Kemp for the frequentist test and Basu for the Bayesian test, and some auxiliary scripts.
Proper citation: kempbasu (RRID:SCR_024055) Copy
https://sourceforge.net/projects/placnet/
Software Perl tools for plasmid analysis in NGS projects.Identifies, visualizes and analyzes plasmids in WGS projects by creating a network of contig interactions, thus allowing comprehensive plasmid analysis within WGS datasets.Optimized to work with Illumina sequences but it also works with 454, Iontorrent or any of the actual sequence technologies. The input of placnet is a set of contigs and one or more SAM files with the mapping of the reads against the contigs. Placnet obtains a set of files, easily opened on Cytoscape software or other network tools.
Proper citation: Placnet (RRID:SCR_024176) Copy
https://prinseq.sourceforge.net/
Software Perl application for quality control and data preprocessing of genomic and metagenomic datasets. Used to filter, reformat, or trim genomic and metagenomic sequence data. Generates summary statistics of sequences in graphical and tabular format.
Proper citation: PRINSEQ (RRID:SCR_024178) Copy
https://sourceforge.net/projects/poamsa/
Software application for multiple sequence alignment in bioinformatics. Has superior ability to handle branching / indels in the alignment.
Proper citation: POA (RRID:SCR_024172) Copy
https://plip-tool.biotec.tu-dresden.de/plip-web/plip/index
Software application as protein�ligand interaction profiler to identify non-covalent interactions between biological macromolecules and their ligands. Provides atom level information on binding characteristics as well as publication ready visualizations and parsable output files. PLIP web tool is based on PLIP command line tool and offers graphical interface for analysis of few structures.
Proper citation: PLIP (RRID:SCR_024173) 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
https://github.com/silx-kit/pyFAI
Open source Python software package designed to perform azimuthal integration and, correspondingly, two-dimensional regrouping on area-detector frames for small- and wide-angle X-ray scattering experiments.
Proper citation: pyFAI (RRID:SCR_024186) 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/rvalieris/parallel-fastq-dump
Software wrapper to speed up downloading process by dividing the work into multiple threads.
Proper citation: parallel-fastq-dump (RRID:SCR_024150) Copy
https://github.com/ggonnella/gfapy
Software library for handling sequence graphs in Python.
Proper citation: GfaPy (RRID:SCR_024030) Copy
https://github.com/FlorianThibord/OptimiR
Software miRSeq data alignment workflow. Used to integrate genetic information to assess the impact of variants on miRNA expression. Used for integrating genome wide genotype data into miRNA sequence alignment analysis.
Proper citation: OptimiR (RRID:SCR_024149) Copy
https://github.com/intake/intake
Software package for finding, investigating, loading and disseminating data.
Proper citation: Intake (RRID:SCR_024042) 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
https://github.com/FePhyFoFum/phyx
Software phylogenetic tools for unix. Used to perform phylogenetics analyses on trees and sequences. Collection of programs written in C ++ to explore, manipulate, analyze and simulate phylogenetic objects.
Proper citation: Phyx (RRID:SCR_024164) Copy
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