Tools   Select Another Resource Report Type

https://github.com/pybel

Software Python package for parsing, validating, compiling, and converting networks encoded in Biological Expression Language.Package consists of network data container, parser and validator, network database manager, data converter and network visualizer. Computational framework for Biological Expression Language. Used to pars BEL documents, validate their semantics, and facilitate data interchange between common formats and database systems like JSON, CSV, Excel, SQL, CX, and Neo4J.

Proper citation: PyBEL (RRID:SCR_017660) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/jdidion/atropos

Software tool for specific, sensitive, and speedy trimming of NGS reads.

Proper citation: Atropos (RRID:SCR_023962) Copy   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/biod/BioD

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/ggonnella/gfapy

Software library for handling sequence graphs in Python.

Proper citation: GfaPy (RRID:SCR_024030) Copy   

•   Source: SciCrunch Registry

http://www.bioimagexd.net/

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   

•   Source: SciCrunch Registry

http://www.bali-phy.org

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   

•   Source: SciCrunch Registry

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   

•   Source: SciCrunch Registry

https://github.com/intake/intake

Software package for finding, investigating, loading and disseminating data.

Proper citation: Intake (RRID:SCR_024042) Copy   

•   Source: SciCrunch Registry