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https://github.com/ggonnella/gfapy
Software library for handling sequence graphs in Python.
Proper citation: GfaPy (RRID:SCR_024030) 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
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://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
https://github.com/andersen-lab/ivar
Software package for viral amplicon based sequencing. Additional tools for metagenomic sequencing are actively being incorporated into iVar.Contains intersection of functionality from multiple tools that are required to call iSNVs and consensus sequences from viral sequencing data across multiple replicates.Following functions are implemented in iVar: trimming of primers and low-quality bases; consensus calling; variant calling both iSNVs and insertions/deletions; identifying mismatches to primer sequences and excluding the corresponding reads from alignment files.
Proper citation: iVar (RRID:SCR_024045) Copy
Open source software for image computation with main focus on high performance volumetric registration, segmentation, and image processing of volumetric medical images.
Proper citation: Plastimatch (RRID:SCR_024168) Copy
Software command line utility and library for lossy compression of PNG images. The conversion reduces file sizes significantly and preserves full alpha transparency. Generated images are compatible with all web browsers and operating systems.
Proper citation: pngquant (RRID:SCR_024169) Copy
https://github.com/BIMSBbioinfo/pigx_rnaseq
Software reproducible genomics analysis pipelines with GNU Guix. Used for analysis of RNA sequencing, chromatin immunoprecipitation sequencing, bisulfite-treated DNA sequencing, and single-cell resolution RNA sequencing. All pipelines process raw experimental data and generate reports containing publication-ready plots and figures, with interactive report elements and standard observables.
Proper citation: PiGx-RNAseq (RRID:SCR_024160) Copy
https://github.com/scottgigante/picopore
Software tool for reducing the storage size of Oxford Nanopore Technologies datasets without loss of functionality.
Proper citation: picopore (RRID:SCR_024161) Copy
Platform independent JAVA software for analysis of sequence based typing methods that generate allelic profiles and their associated epidemiological data.Phylogenetic inference and data visualization for sequence based typing methods.
Proper citation: PHYLOViZ (RRID:SCR_024162) Copy
https://changeo.readthedocs.io
Collection of software tools for processing the output of V(D)J alignment tools, assigning clonal clusters to immunoglobulin Ig sequences, and reconstructing germline sequences.
Proper citation: Change-O (RRID:SCR_023986) 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
https://genome.sph.umich.edu/wiki/C++_Library:_libStatGen
Software library as set of classes for creating statistical genetic programs.
Proper citation: libStatGen (RRID:SCR_024093) Copy
https://github.com/rvaser/thread_pool
Software C++ thread pool library.
Proper citation: ThreadPool (RRID:SCR_024094) Copy
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