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https://bioconductor.org/packages/fgsea/
Software R package for fast preranked gene set enrichment analysis. Allows to make more permutations and get more fine grained p-values, which allows to use accurate stantard approaches to multiple hypothesis correction.
Proper citation: fgsea (RRID:SCR_020938) Copy
Portal enables browsing, searching, and analysis of human genetic information linked to common metabolic diseases and traits, while protecting integrity and confidentiality of underlying data. Aggregates and analyzes genetic association results, epigenomic annotations, and results of computational prediction methods to provide data, visualizations, and tools in open access portal.
Proper citation: Common Metabolic Diseases Knowledge Portal (RRID:SCR_020937) Copy
https://CRAN.R-project.org/package=ez
Software statistical analysis R package used for easy analysis and visualization of factorial experiments. Provides interface to common analysis techniques, including analysis of variance and mixed effects modeling. Visualization functions also include design visualization for pre-analysis data auditing, and correlation matrix visualization. Package includes functions for non-parametric analysis, including permutation tests and bootstrap resampling.
Proper citation: ez (RRID:SCR_020990) Copy
https://github.com/r3fang/SnapATAC
Software package for analyzing scATAC-seq datasets.Used to dissects cellular heterogeneity in unbiased manner and map trajectories of cellular states. Can process data from up to million cells. Incorporates existing tools into comprehensive package for analyzing single cell ATAC-seq dataset.
Proper citation: SnapATAC (RRID:SCR_020981) Copy
http://cqb.pku.edu.cn/ZhuLab/DeePhage
Software tool to distinguish virulent and temperate phage derived sequences in metavirome data with deep learning approach. Used to identify virome sequences as temperate phage derived or virulent phage derived fragments.
Proper citation: DeePhage (RRID:SCR_019243) Copy
Open source software platform for studying fruit fly brain function, and for investigating fruit fly brain disease models that are highly relevant to mechanisms of human neurological and psychiatric disorders. Collaborative ecosystem for accelerating discovery of functional logic of fruit fly brain. Includes FlyBrainLab and BrainMapsViz. Stores and integrates fruit fly brain research data. Repository of tools and methods to build, emulate and compare fruit fly brain models in health and disease. Open framework for fruit fly brain data processing and model execution.
Proper citation: Fruit Fly Brain Observatory (RRID:SCR_019244) Copy
https://github.com/pensoft/omicsdatapaper
Software package for streamlined import of omics metadata from European Nucleotide Archive into OMICS Data Paper manuscript. Omics Data Paper R Shiny app demonstrates workflow for automatic import of ENA genomic metadata into omics data paper manuscript. Streamlined conversion of metadata into manuscript facilitates authoring of omics data papers, which allow omics dataset creators to receive credit for their work and to improve description and visibility of their datasets.
Proper citation: Omics Data Paper Generator (RRID:SCR_019809) Copy
Software package contains data analysis and processing tools required for rapid and effective interrogation of imaging data. Allows for full integration of full spectrum molecular imaging experiments on SYNAPT family platforms, as well as DESI imaging on Xevo G2-XS QTof Mass Spectrometers, using single user interface.
Proper citation: Waters High Definition Imaging (RRID:SCR_021054) Copy
https://www.fluidigm.com/singlearticles/cytof-software-upgrade-7dot0
Software for analyzing mass cytometry (CyTOF) data.
Proper citation: Fluidigm CyTOF (RRID:SCR_021055) Copy
https://www.synapse.org/#!Synapse:syn22345748/wiki/605339
Reference dataset of multiplexed immunofluorescence microscopy images collected at HMS Laboratory of Systems Pharmacology. Includes set of images of different types for development and benchmarking of computational methods for image processing. As of 4/2/2021, EMIT comprises tissue microarray containing cores from 34 cancer, non-neoplastic diseases, and normal tissue collected from clinical discards under IRB supervised protocol. TMA was imaged using cyclic immunofluorescence method. Additional extensions of EMIT are currently in the planning stages. Long term goal is to compose ImageNet like resource for highly multiplexed images of tissues and tumors by consolidating high quality curated datasets.
Proper citation: Exemplar Microscopy Images of Tissues (RRID:SCR_021052) Copy
https://github.com/HMS-IDAC/UnMicst
Software tool as set of deep learning nuclei instance and semantic segmentation models that have been trained on 6 human tissue types: tonsil, small intestine, ovary, and cancers of brain, colon, prostate, and lung stained with Hoechst 33342 and combination of lamin B2 and nucleoporin98. Includes manually curated annotations as well as novel concept of introducing intentionally defocused and saturated images for robustness.
Proper citation: UnMICST (RRID:SCR_021050) Copy
Software tool to open and assess stereolithographic data. Software application tailored for additive manufacturing, rapid prototyping, and 3D printing.
Proper citation: Autodesk Netfabb Premium (RRID:SCR_019812) Copy
Open access software platform to faciliate calculation of quantities related to light and lighting. Users can upload spectra and platform will calculate relevant quantites including luminance, chromaticity, and α-opic radiance and α-opic daylight luminances from spectra, generate visualisation of spectrum, and enable export of calculations in tabular form.
Proper citation: luox (RRID:SCR_020994) Copy
https://github.com/ylab-hi/ScanNeo
Open software pipeline for analyzing RNA-seq to predict neoepitopes derived from small to large sized indels. Used for identifying indel derived neoantigens using RNA-Seq data.
Proper citation: ScanNeo (RRID:SCR_019253) Copy
https://gitlab.com/PAM-PIE/PAM
Software package for quantitative analysis of fluorescence microscopy and spectroscopy data, with focus on experiments using pulsed interleaved excitation. Open source software package written in MATLAB that offers workflow through its graphical user interface. Framework for integrated analysis of imaging, single-molecule, and ensemble fluorescence data.Supports most types of data collection modalities.
Proper citation: PAM (RRID:SCR_020966) Copy
https://www.leicabiosystems.com/digital-pathology/scan/aperio-versa/
Software tool designed to support Leica Biosystems Aperio VERSA scanner. Digital pathology scanning software. Used for diverse imaging needs for digital pathology.
Proper citation: Aperio VERSA (RRID:SCR_021016) Copy
https://cran.r-project.org/web/packages/igraph/
Software package for graphs and network analysis. Provides functions for generating random and regular graphs, graph visualization, centrality methods and much more.Can be programmed in R, Python, Mathematica, C/C Plus Plus.
Proper citation: igraph (RRID:SCR_019225) Copy
https://www.bmglabtech.com/mars-data-analysis-software/
Proprietary software package for data analysis by BMG Labtech.
Proper citation: MARS Data Analysis Software (RRID:SCR_021015) Copy
https://driftage.readthedocs.io/
Software tool as modular multi agent framework to detect concept drifts from batch or streaming data.
Proper citation: Driftage (RRID:SCR_021031) Copy
https://www.ebi.ac.uk/pdbe/emdb/empiar/
Public archive for raw electron microscopy image data. Resource for raw 2D electron microscopy images. Used to browse, upload and download raw images to build 3D structure. Provides access to raw data to facilitate methods development and validation. Complements Electron Microscopy Data Bank where 3D volumes are stored, and uses Aspera platform for data transfers.
Proper citation: Electron Microscopy Public Image Archive (RRID:SCR_019237) Copy
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