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Patrick Kimes' misc. functions

Modeled after Karl Broman's broman package.

Patrick Kimes's Projects

benchmark-fdr icon benchmark-fdr

Benchmarking study of recent covariate-adjusted FDR methods

book icon book

Compiled and pretty version of labs

dfci-intror icon dfci-intror

Code and data for DFCI seminar - Introduction to R and RStudio

glmargin icon glmargin

generalized large-margin classification

labs icon labs

Rmd source files for the HarvardX series PH525x

mitie icon mitie

The RNA-seq transcript predictor for multiple samples

notebooks icon notebooks

Notebooks and resources for the Tokyo Datathon 2023

pynbs icon pynbs

Python 2.7 implementation of network-based stratification (NBS) algorithm from Hofree et al (Nature Methods 2013)

salmon icon salmon

🐟 🍣 🍱 Highly-accurate & wicked fast transcript-level quantification from RNA-seq reads using lightweight alignments

shoal icon shoal

Improved multi-sample transcript abundance estimates using adaptive priors

sigclust2 icon sigclust2

tests for statistical significance of clustering

sigfuge icon sigfuge

Significance of clustering in per-base pileups

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