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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/mlinderm/npsv
Software Python tool for standalone genotyping of deletion and insertion structural variants in short read whole genome sequencing data. Implements machine learning based approach for SV genotyping that employs NGS simulation to model the combined effects of the genomic region, sequencer and alignment pipeline.
Proper citation: NPSV (RRID:SCR_020984) 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
https://satijalab.org/signac/index.html
Software framework for analysis of single cell chromatin data. Used for analysis, interpretation, and exploration of single cell chromatin datasets including datasets that co-assay DNA accessibility with gene expression, protein abundance, and mitochondrial genotype. Analysis of single-cell chromatin data including peak calling, quantification, quality control, dimension reduction, clustering, integration with single-cell gene expression datasets, DNA motif analysis, and interactive visualization.
Proper citation: Signac (RRID:SCR_021158) 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
https://github.com/aidenlab/Juicebox
Visualization and analysis software for Hi-C data.
Proper citation: Juicebox (RRID:SCR_021172) 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://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://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://github.com/bahanonu/ciatah
Software package for analyzing one and two photon calcium imaging datasets.Can be used to create GUI-less, command line ready analysis pipelines. Supports Neurodata Without Borders data standard for reading/writing cell-extraction (e.g. outputs of PCA-ICA, CELLMax, CNMF, CNMF-E, EXTRACT, etc.). Supports reading and writing NWB movie files with continued integration planned. Supports most major imaging movie file formats: HDF5, NWB, AVI, ISXD [Inscopix], and TIFF.
Proper citation: calciumImagingAnalysis (RRID:SCR_021153) 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://caiman.readthedocs.io/
Software Python toolbox for large scale calcium imaging data analysis and behavioral analysis.Used for motion correction, source extraction, spike deconvolution, and component registration across multiple days. It is suitable for both two-photon and one-photon fluorescence microscopy data, and can be run in both batch and online modes. Contains some routines for analysis of behavior from video cameras.
Proper citation: CaImAn (RRID:SCR_021152) Copy
https://github.com/sciensic/SCIGA
Software Perl toolkit for 10X single cell immunoglobulin repertoires analysis. Uses raw reads or output of Cellranger as input and performs reads quality control, immunoglobulin sequence assembly, sequence annotation, heavy- and light- chain pairing, computing statistics and visualizing.
Proper citation: SCIGA (RRID:SCR_021002) Copy
http://sycamore.h-its.org/sycamore/
Web browser based application that facilitates construction, simulation and analysis of kinetic models in systems biology. Allows database supported modelling, basic model checking and estimation of unknown kinetic parameters based on protein structures. Integrates different online applications as well as locally installed software. Provides user guidance for sequence of steps associated with model building, model checking, simulation and analysis of results.
Proper citation: SYCAMORE (RRID:SCR_021117) Copy
Software R package of igraph network analysis library.
Proper citation: igraph for R (RRID:SCR_021238) Copy
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