misha - Toolkit for Analysis of Genomic Data
A toolkit for analysis of genomic data. The 'misha' package implements an efficient data structure for storing genomic data, and provides a set of functions for data extraction, manipulation and analysis. Some of the 2D genome algorithms were described in Yaffe and Tanay (2011) <doi:10.1038/ng.947>.
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genomic-data-analysiszlibcpp
8.53 score 4 stars 1 dependents 159 scripts 317 downloadstgstat - Amos Tanay's Group High Performance Statistical Utilities
A collection of high performance utilities to compute distance, correlation, auto correlation, clustering and other tasks. Contains graph clustering algorithm described in "MetaCell: analysis of single-cell RNA-seq data using K-nn graph partitions" (Yael Baran, Akhiad Bercovich, Arnau Sebe-Pedros, Yaniv Lubling, Amir Giladi, Elad Chomsky, Zohar Meir, Michael Hoichman, Aviezer Lifshitz & Amos Tanay, 2019 <doi:10.1186/s13059-019-1812-2>).
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algorithms-implementedcorrelationknnstatisticsopenblascpp
7.03 score 8 stars 1 dependents 37 scripts 345 downloadstglkmeans - Efficient Implementation of K-Means++ Algorithm
Efficient implementation of K-Means++ algorithm. For more information see (1) "kmeans++ the advantages of the k-means++ algorithm" by David Arthur and Sergei Vassilvitskii (2007), Proceedings of the eighteenth annual ACM-SIAM symposium on Discrete algorithms, Society for Industrial and Applied Mathematics, Philadelphia, PA, USA, pp. 1027-1035, and (2) "The Effectiveness of Lloyd-Type Methods for the k-Means Problem" by Rafail Ostrovsky, Yuval Rabani, Leonard J. Schulman and Chaitanya Swamy <doi:10.1145/2395116.2395117>.
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algorithms-implementedkmeanscpp
6.10 score 7 stars 30 scripts 272 downloadsshaman - Sampling Hi-C Contact Matrices for Aparametric Normalization
Generate expected Hi-C (genome-wide chromosome conformation capture) data maintaining marginal coverage, and the decay in contact probability with increasing genomic distance. Expected Hi-C data is used for normalization and graphical presentation of statistical significance of observed Hi-C contact enrichments. The method is described in Mendelson Cohen et al. (2017) <doi:10.1101/187203>.
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hi-cmishacpp
5.77 score 6 stars 49 scripts 112 downloadsnaryn - Native Access Medical Record Retriever for High Yield Analytics
A toolkit for medical records data analysis. The 'naryn' package implements an efficient data structure for storing medical records, and provides a set of functions for data extraction, manipulation and analysis.
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data-analysismedical-recordscpp
5.48 score 3 stars 4 scripts 242 downloadsslanter - Slanted Matrices and Ordered Clustering
Slanted matrices and ordered clustering for better visualization of similarity data.
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4.88 score 5 stars 1 dependents 7 scripts 264 downloadsjlview - Zero-Copy Julia to R Array Bridge via ALTREP
Provides zero-copy R views of Julia-owned arrays by implementing ALTREP (Alternative Representations) classes that return pointers directly into Julia's memory. The package integrates with 'JuliaCall' and uses C-level finalizers for safe cross-runtime garbage collection.
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4.70 score 5 stars 8 scripts 200 downloads