Michael Love

Michael Love

1 packages on CRAN

2 packages on GitHub

4 packages on Bioconductor

DESeq2

bioconductor
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Estimate variance-mean dependence in count data from high-throughput sequencing assays and test for differential expression based on a model using the negative binomial distribution.

exomeCopy

bioconductor
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Detection of copy number variants (CNV) from exome sequencing samples, including unpaired samples. The package implements a hidden Markov model which uses positional covariates, such as background read depth and GC-content, to simultaneously normalize and segment the samples into regions of constant copy count.

alpine

github
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Fragment sequence bias modeling and correction for RNA-seq transcript abundance estimation.

dagdata

github
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Data Analysis for Genomics datasets

tximport

bioconductor
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Imports transcript-level abundance, estimated counts and transcript lengths, and summarizes into matrices for use with downstream gene-level analysis packages. Average transcript length, weighted by sample-specific transcript abundance estimates, is provided as a matrix which can be used as an offset for different expression of gene-level counts.

GenomicFiles

bioconductor
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This package provides infrastructure for parallel computations distributed 'by file' or 'by range'. User defined MAPPER and REDUCER functions provide added flexibility for data combination and manipulation.

rafalib

cran
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A series of shortcuts for routine tasks originally developed by Rafael A. Irizarry to facilitate data exploration.