philentropy - Similarity and Distance Quantification Between Probability Functions
Computes 46 optimized distance and similarity measures for comparing probability functions (Drost (2018) <doi:10.21105/joss.00765>). These comparisons between probability functions have their foundations in a broad range of scientific disciplines from mathematics to ecology. The aim of this package is to provide a core framework for clustering, classification, statistical inference, goodness-of-fit, non-parametric statistics, information theory, and machine learning tasks that are based on comparing univariate or multivariate probability functions.
Last updated
distance-measuresdistance-quantificationinformation-theoryjensen-shannon-divergenceparametric-distributionssimilarity-measuresstatisticscpp
12.82 score 150 stars 17 dependents 774 scripts 5.8k downloads
myTAI - Evolutionary Transcriptomics
Investigate the evolution of biological processes by capturing evolutionary signatures in transcriptomes (Drost et al. (2018) <doi:10.1093/bioinformatics/btx835>). This package aims to provide a transcriptome analysis environment to quantify the average evolutionary age of genes contributing to a transcriptome of interest.
Last updated
biological-processesconservationevo-devoevolutionevolutionary-transcriptomicsexpression-profilesgene-expressiongene-setsmytaistudies-transcriptomestranscriptomecpp
9.92 score 48 stars 121 scripts 627 downloadsbiomartr - Genomic Data Retrieval
Perform large scale genomic data retrieval and functional annotation retrieval. This package aims to provide users with a standardized way to automate genome, proteome, 'RNA', coding sequence ('CDS'), 'GFF', and metagenome retrieval from 'NCBI RefSeq', 'NCBI Genbank', 'ENSEMBL', and 'UniProt' databases. Furthermore, an interface to the 'BioMart' database (Smedley et al. (2009) <doi:10.1186/1471-2164-10-22>) allows users to retrieve functional annotation for genomic loci. In addition, users can download entire databases such as 'NCBI RefSeq' (Pruitt et al. (2007) <doi:10.1093/nar/gkl842>), 'NCBI nr', 'NCBI nt', 'NCBI Genbank' (Benson et al. (2013) <doi:10.1093/nar/gks1195>), etc. with only one command.
Last updated
biomartgenomic-data-retrievalannotation-retrievaldatabase-retrievalncbiensemblbiological-data-retrievalensembl-serversgenomegenome-annotationgenome-retrievalgenomicsmeta-analysismetagenomicsncbi-genbankpeer-reviewedproteomesequenced-genomes
9.91 score 226 stars 3 dependents 1.3k downloads