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A software tool used for functional enrichment and interaction network analysis of genes and proteins. Users can search against a default background database or load customized database. The results can be depicted as venn, bar, column, pie and doughnut charts.
Proper citation: FunRich: Functional Enrichment analysis tool (RRID:SCR_014467) Copy
Data aggregate that compiles results from bioinformatics analyses across multiple samples into a single report. It is written in Python.
Proper citation: MultiQC (RRID:SCR_014982) Copy
http://bioconductor.org/packages/release/bioc/html/topGO.html
Software package which provides tools for testing GO terms while accounting for the topology of the GO graph. Different test statistics and different methods for eliminating local similarities and dependencies between GO terms can be implemented and applied.
Proper citation: topGO (RRID:SCR_014798) Copy
https://sites.google.com/site/danposdoc/
Software toolkit with various functions for the analysis of nucleosome and protein occupancy by sequencing.
Proper citation: DANPOS2 (RRID:SCR_015527) Copy
http://compbio.cs.princeton.edu/concavity/
Software for predicting protein ligand binding sites that integrate evolutionary sequence conservation estimates with structure-based methods for identifying protein surface cavities. Used in predicting catalytic sites and drug binding pockets.
Proper citation: Concavity (RRID:SCR_016063) Copy
https://github.com/HASTE-project
Software toolkit for rapid development of cloud native intelligent data pipelines for scientific data streams. Hierarchical approach to acquisition, analysis, and interpretation of image data. Developed in the project Hierarchical Analysis of Spatial and Temporal Data.
Proper citation: HASTE-project (RRID:SCR_020932) Copy
https://mermaid.readthedocs.io/en/latest/
Registration toolbox written in pyTorch. Supports various image registration methods. Focuses on nonparametric registration approaches including stationary velocity fields and large discplacement diffeomorphic metric mapping models though simple affine registration is also possible. Allows for rapid prototyping of new image registration approaches and similarity measures.
Proper citation: MERMAID (RRID:SCR_020939) Copy
https://github.com/theislab/scvelo
Software package for estimating and analyzing RNA velocities in single cells using dynamical modeling. RNA Velocity using dynamical modeling.
Proper citation: scVelo (RRID:SCR_018168) Copy
https://github.com/Ecogenomics/GtdbTk
Open source software tool for assigning objective taxonomic classifications to bacterial and archaeal genomes based on Genome Database Taxonomy. Designed to work with recent advances that allow metagenome assembled genomes to be obtained directly from environmental samples. Can also be applied to isolate and single cell genomes.
Proper citation: GTDB-Tk (RRID:SCR_019136) Copy
Software tool for genome and metagenome distance estimation using MinHash. Reduces large sequences and sequence sets to small, representative sketches, from which global mutation distances can be rapidly estimated.
Proper citation: Mash (RRID:SCR_019135) Copy
https://www.bioconductor.org/packages/release/bioc/html/ensembldb.html
Software R package to create and use Ensembl based annotation resources.
Proper citation: ensembldb (RRID:SCR_019103) Copy
https://gitlab.com/biomerieux-data-science/clustlasso
Software R package to build predictive signatures of microbial phenotypes. Software package implementing cluster lasso approach.
Proper citation: clustLasso (RRID:SCR_018820) Copy
Interactive Python based interface to Rosetta molecular modeling suite. Stand alone Python based implementation of Rosetta molecular modeling package that allows users to write custom structure prediction and design algorithms using major Rosetta sampling and scoring functions.
Proper citation: PyRosetta (RRID:SCR_018541) Copy
https://github.com/AdmiralenOla/Scoary
Software tool that scores components of pan genome for associations to observed phenotypic traits while accounting for population stratification, with minimal assumptions about evolutionary processes.Designed to take gene presence absence.csv file from Roary as well as traits file created by user and calculate associations between all genes in accessory genome and traits. It reports list of genes sorted by strength of association per trait.
Proper citation: Scoary (RRID:SCR_021087) Copy
https://github.com/big-data-lab-team/spot
Open source software tool for file based localization of numerical perturbations in data analysis pipelines. Identifies components in pipeline, at resolution level of system process, that produce different results in different execution conditions.
Proper citation: Spot (RRID:SCR_018915) Copy
https://cran.r-project.org/web/packages/GALLO/vignettes/GALLO.html
Software R package developed for accurate annotation of genes and quantitative trait loci located in regions identified in common genomic analyses performed in livestock, such as Genome Wide Association Studies and transcriptomics using RNA-Sequencing. Allows graphical visualization of gene and QTL annotation results, data comparison among different grouping factors like methods, breeds, tissues, statistical models, studies and QTL enrichment in different livestock species including cattle, pigs, sheep, and chickens.
Proper citation: Genomic Annotation in Livestock for positional candidate LOci (RRID:SCR_019212) Copy
https://github.com/SMI/SmiServices
Software suite of tools for cataloguing and anonymising DICOM files, as used for Scottish Medical Imaging project. Software suite of microservices for loading, anonymising, linking and extracting large volumnes of dicom medical images to support medical research. Platform allows dicom tags extracted from clinical images to be loaded into MongoDB and relational database tables for purposes of generating anonymous linked research extracts including image anonymisation.
Proper citation: SMI Services (RRID:SCR_018881) Copy
https://cran.r-project.org/package=psych
Software R package for multivariate analysis and scale construction using factor analysis, principal component analysis, cluster analysis and reliability analysis.Procedures for Psychological, Psychometric, and Personality Research. Used for personality, psychometric theory and experimental psychology.
Proper citation: psych (RRID:SCR_021744) Copy
Comprehensive antibiotic resistance database. Bioinformatic database of resistance genes, their products and associated phenotypes.
Proper citation: CARD (RRID:SCR_023995) Copy
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