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iscream - Make fast and memory efficient BED file queries, summaries and matrices

BED files store ranged genomic data that can be queried even when the files are compressed. iscream can query data from BED files and return them in muliple formats: parsed records or their summary statistics as data frames or GenomicRanges objects, and matrices as matrix, GenomicRanges, or SummarizedExperiment objects. iscream also provides specialized support for importing methylation data.

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dataimportsoftwaresequencingsinglecelldnamethylationbedrcpptabixwgbscurlbzip2xz-utilszlibcppopenmp

6.29 score 12 scripts 212 downloads

ceas - Cellular Energetics Analysis Software

Measuring cellular energetics is essential to understanding a matrix’s (e.g. cell, tissue or biofluid) metabolic state. The Agilent Seahorse machine is a common method to measure real-time cellular energetics, but existing analysis tools are highly manual or lack functionality. The Cellular Energetics Analysis Software (ceas) R package fills this analytical gap by providing modular and automated Seahorse data analysis and visualization using the methods described by Mookerjee et al. (2017) <doi:10.1074/jbc.m116.774471>.

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4.30 score 2 stars 3 scripts 215 downloads