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https://github.com/schneebergerlab/syri
SyRI compares alignments between two chromosome level assemblies and identifies synteny and structural rearrangements.
Proper citation: SyRI (RRID:SCR_023008) Copy
https://cell-innovation.nig.ac.jp/maser/Tools/visualization_top_en.html
One stop platform for NGS big data from analysis to visualization. There are about 400 analysis pipelines integrated on Maser. List of all analysis pipelines, including descriptions and approximate execution times, can be found on page for ‘All pipelines’ in the User Guide. loadGffToGe_db for custom genome software loads GFF files of custom genomes to a database for Genome Explorer. It allows the user to browse the results through the GE.
Proper citation: loadGffToGe_db for custom genome (RRID:SCR_015997) Copy
Software tool as a cross-platform NIfTI format image viewer. Used for viewing and exporting of brain images. MRIcroGL is a variant of MRIcron.
Proper citation: MRIcron (RRID:SCR_002403) Copy
https://github.com/Malindrie/scShapes
Software tool as statistical framework for identifying distribution shapes in single-cell RNA-sequencing data.
Proper citation: scShapes (RRID:SCR_022838) Copy
https://www.palisade.com/risk/
Software is add-in tool for Microsoft Excel that computes and tracks many different possible scenarios in model using Monte Carlo simulation.Helps make better decisions through risk modeling and analysis.
Proper citation: atRISK (RRID:SCR_022837) Copy
https://github.com/spoonsso/dannce
Convolutional neural network that calculates 3D positions of user-defined anatomical landmarks on behaving animals from videos taken at multiple angles. Works on recorded video data from multiple cameras. Used for 3D markerless pose estimation and tracking.
Proper citation: DANNCE (RRID:SCR_023061) Copy
Center whose goals include fostering collaboration among basic and clinical investigators, facilitating the use of new technologies in the study of treatment of digestive diseases, and providing education and training for improved treatment and diagnosis.
Proper citation: University of Chicago Digestive Diseases Research Core Center (RRID:SCR_015601) Copy
Software Python framework designed to work with multimodal omics data. Aims to provide convenience and speed to its users enabling standardised analysis while staying flexible and expandable. Muon stands on shoulders of and integrates with annotated data object specification and scanpy library for single cell analysis in Python.
Proper citation: MUON (RRID:SCR_022804) Copy
Web service for statistics with automated data analysis mode.
Proper citation: StatTech (RRID:SCR_023071) Copy
http://www.bioconductor.org/packages/release/bioc/html/RMassBank.html
Workflow software to process tandem MS files and build MassBank records. Functions include automated extraction of tandem MS spectra, formula assignment to tandem MS fragments, recalibration of tandem MS spectra with assigned fragments, spectrum cleanup, automated retrieval of compound information from Internet databases, and export to MassBank records.
Proper citation: RMassBank (RRID:SCR_002797) Copy
https://github.com/Lcornet/GENERA
Software toolbox to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes.
Proper citation: GENERA (RRID:SCR_023113) Copy
https://www.distillersr.com/products/distillersr-systematic-review-software
Literature review software by DistillerSR Inc. Automates management of literature collection, screening, and assessment using AI and intelligent workflows. From systematic literature review to rapid review to living review, makes any project simpler to manage and configure to produce transparent, audit-ready, and compliant results.
Proper citation: DistillerSR (RRID:SCR_023078) Copy
https://github.com/ChristopherWilks/megadepth
Software tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files.Quantifies number of RNA-seq reads assigned to gene in BAM file, successor of bamcounts.
Proper citation: Megadepth (RRID:SCR_022779) Copy
https://github.com/Whitlock-Group/HERBS
Open source, extendable, intuitive and interactive software platform for image visualisation and image registration. Python based GUI for histological E-data registration in brain space.
Proper citation: Histological E data Registration in rodent Brain Spaces (RRID:SCR_022776) Copy
Simple Western instrument software to analyze assay data and processes results.
Proper citation: Compass for Simple Western (RRID:SCR_022930) Copy
https://CRAN.R-project.org/package=ggsignif
Software package to indicate if two groups are significantly different. Used to add significance brackets to ggplots.
Proper citation: ggsignif (RRID:SCR_023047) Copy
https://github.com/Genomon-Project
Software DNA and RNA sequence analysis pipeline.
Proper citation: GenomonPipeline (RRID:SCR_022989) Copy
https://github.com/vdemichev/DiaNN
Software tool for processing of data independent acquisition proteomics experiments. Universal automated software suite for DIA proteomics data analysis. Neural networks and interference correction enable deep proteome coverage in high throughput.
Proper citation: DIA-NN (RRID:SCR_022865) Copy
https://github.com/nextgenusfs/funannotate
Software package for genome annotation. Built specifically for fungi, but will also work with higher eukaryotes. Used for genome prediction, annotation, and comparison.
Proper citation: funannotate (RRID:SCR_023039) Copy
https://github.com/open2c/pairtools
Software command line framework to process sequencing data from Hi-C experiment. Used to process pair end sequence alignments.
Proper citation: pairtools (RRID:SCR_023038) Copy
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