genomation - Summary, annotation and visualization of genomic data
A package for summary and annotation of genomic intervals. Users can visualize and quantify genomic intervals over pre-defined functional regions, such as promoters, exons, introns, etc. The genomic intervals represent regions with a defined chromosome position, which may be associated with a score, such as aligned reads from HT-seq experiments, TF binding sites, methylation scores, etc. The package can use any tabular genomic feature data as long as it has minimal information on the locations of genomic intervals. In addition, It can use BAM or BigWig files as input.
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annotationsequencingvisualizationcpgislandcpp
11.47 score 79 stars 5 dependents 784 scripts 1.4k downloadsnetSmooth - Network smoothing for scRNAseq
netSmooth is an R package for network smoothing of single cell RNA sequencing data. Using bio networks such as protein-protein interactions as priors for gene co-expression, netsmooth improves cell type identification from noisy, sparse scRNAseq data.
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networkgraphandnetworksinglecellrnaseqgeneexpressionsequencingtranscriptomicsnormalizationpreprocessingclusteringdimensionreductionbioinformaticsgenomicssingle-cell
7.44 score 29 stars 4 scripts 398 downloadsImageArray - A framework for on-disk and in-memory image arrays
ImageArray provides a framework for on-disk and in-memory image arrays, specifically for pyramidal images stored in HDF5, Zarr and life sciences image file formats (OME Bio-Formats).
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softwarevisualization
7.05 score 6 stars 2 dependents 15 scripts 251 downloadsBPCells - Single Cell Counts Matrices to PCA
> Efficient operations for single cell ATAC-seq fragments and RNA counts matrices. Interoperable with standard file formats, and introduces efficient bit-packed formats that allow large storage savings and increased read speeds.
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zlibhdf5cpp
6.61 score 5 dependents 700 scriptsVoltRon - VoltRon for Spatial Omics Data Integration and Analysis
VoltRon is a spatial omic analysis toolbox for multi-omics integration using spatial image registration. VoltRon is capable of analyzing multiple types and modalities of spatially-aware datasets. VoltRon visualizes and analyzes regions of interests (ROIs), spots, cells, molecules and event tiles.
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opencvcpp
6.31 score 121 stars 80 scriptsdeconvR - Simulation and Deconvolution of Omic Profiles
This package provides a collection of functions designed for analyzing deconvolution of the bulk sample(s) using an atlas of reference omic signature profiles and a user-selected model. Users are given the option to create or extend a reference atlas and,also simulate the desired size of the bulk signature profile of the reference cell types.The package includes the cell-type-specific methylation atlas and, Illumina Epic B5 probe ids that can be used in deconvolution. Additionally,we included BSmeth2Probe, to make mapping WGBS data to their probe IDs easier.
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dnamethylationregressiongeneexpressionrnaseqsinglecellstatisticalmethodtranscriptomicsbioconductor-packagedeconvolutiondna-methylationomics
6.10 score 10 stars 21 scripts 460 downloadsanglemania - Feature Extraction for scRNA-seq Dataset Integration
anglemania extracts genes from multi-batch scRNA-seq experiments for downstream dataset integration. It shows improvement over the conventional usage of highly-variable genes for many integration tasks. We leverage gene-gene correlations that are stable across batches to identify biologically informative genes which are less affected by batch effects. Currently, its main use is for single-cell RNA-seq dataset integration, but it can be applied for other multi-batch downstream analyses such as NMF.
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singlecellbatcheffectmultiplecomparisonfeatureextractioncpp
5.51 score 4 stars 2 scripts 222 downloadsHDF5DataFrame - HDF5-backed DataFrame objects and methods
HDF5DataFrame is an R/Bioconductor package for HDF5-backed DataFrame objects and methods. This allows HDF5-backed data to be easily used as data frames with arbitrary sets of columns.
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datarepresentationinfrastructuresoftware
4.08 score 1 stars 2 dependents 1 scriptsRCDT - Fast 2D Constrained Delaunay Triangulation
Performs 2D Delaunay triangulation, constrained or unconstrained, with the help of the C++ library 'CDT'. A function to plot the triangulation is provided. The constrained Delaunay triangulation has applications in geographic information systems.
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cpp
4.07 score 2 dependents 39 scripts 52 downloadsZarrDataFrame - Bioconductor-friendly Bindings for Zarr
Implements bindings for zarr store that are compatible with Bioconductor S4 data structures, namely the DataFrame and DelayedArray. This allows Zarr-backed data to be easily used as data frames with arbitrary sets of columns
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datarepresentationinfrastructuresoftware
2.78 score 2 dependents 1 scriptsHDF5DataFrame - HDF5-backed DataFrame objects and methods
Implements bindings for h5 files that are compatible with Bioconductor S4 data structures, namely the DataFrame and DelayedArray. This allows HDF5-backed data to be easily used as data frames with arbitrary sets of columns.
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datarepresentationinfrastructuresoftware
2.48 score 2 dependents 1 scripts