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r-spark
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public |
SPARK is an efficient tool for identifying spatial expression patterns. SPARK directly models raw count data generated from various spatial resolved transcriptomic techniques. With a new efficient penalized quasi-likelihood based algorithm, SPARK is scalable to data sets with tens of thousands of genes measured on thousands of samples. Build upon a non-parametric framework, SPARK-X is scalable to large-scale data sets with tens of thousands of genes measured on hundred thousands of samples.
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2025-03-25 |
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r-tfbstools
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public |
TFBSTools is a package for the analysis and manipulation of transcription factor binding sites. It includes matrices conversion between Position Frequency Matirx (PFM), Position Weight Matirx (PWM) and Information Content Matrix (ICM). It can also scan putative TFBS from sequence/alignment, query JASPAR database and provides a wrapper of de novo motif discovery software.
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2025-03-25 |
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r-bseqsc
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public |
Companion package to: A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure. Baron et al. Cell Systems (2016) https://www.ncbi.nlm.nih.gov/pubmed/27667365
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2025-03-25 |
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r-meringue
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public |
MERINGUE is a computational framework based on spatial auto-correlation and cross-correlation analysis to identify genes with spatially heterogeneous expression patterns, derive putative cell-cell communication, and perform spatially informed cell clustering in 2D and 3D in a density-agnostic manner using spatially resolved transcriptomics data.
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2025-03-25 |
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r-chromvarmotifs
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public |
Stores several motifs as PWMatrixList objects for use in R with packages like motifmatchr and chromVAR.
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2025-03-25 |
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r-archr
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public |
This package is designed to streamline scATAC analyses in R.
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2025-03-25 |
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r-presto
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public |
Scalable implementation of the Wilcoxon rank sum test and auROC statistic. Interfaces to dense and sparse matrices, as well as genomics analysis frameworks Seurat and SingleCellExperiment.
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2025-03-25 |
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r-harmony
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public |
Implementation of the Harmony algorithm for single cell integration, described in Korsunsky et al <doi.org/10.1101/461954>. Package includes a standalone Harmony function and interfaces to external frameworks.
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2025-03-25 |
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r-nmf
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public |
This package provides a framework to perform Non-negative Matrix Factorization (NMF). It implements a set of already published algorithms and seeding methods, and provides a framework to test, develop and plug new/custom algorithms. Most of the built-in algorithms have been optimized in C++, and the main interface function provides an easy way of performing parallel computations on multicore machines.
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2025-03-25 |
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r-cssam
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public |
Cell-type specific differential expression of a microarray experiment of heterogeneous tissue samples, using SAM.
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2025-03-25 |
