R packages by kaiaragaki

tidyestimate - A Tidy Implementation of 'ESTIMATE'

The 'ESTIMATE' package infers tumor purity from expression data as a function of immune and stromal infiltrate, but requires writing of intermediate files, is un-pipeable, and performs poorly when presented with modern datasets with current gene symbols. 'tidyestimate' a fast, tidy, modern reimagination of 'ESTIMATE' (2013) <doi:10.1038/ncomms3612>.

Last updated 1 years ago

cancer-genomicstidy

4.78 score 12 stars 4 scripts 215 downloads

gplate - A Grammar of Plates

`gplate` attempts to provide a succinct yet powerful grammar to describe common microwell layouts to aide in both plotting and tidying.

Last updated 3 months ago

ggplot2

4.56 score 4 stars 3 packages 9 scripts

reclanc - A Revival of the ClaNC Algorithm

Classification of microarrays to nearest centroids (ClaNC) <doi:10.1093/bioinformatics/bti756> selects optimal genes for centroids, similar to Prediction Analysis for Microarrays (PAM) but using fewer corrective factors, resulting in greater sensitivity and accuracy. Unfortunately, the original source of ClaNC can no longer be found. 'reclanc' reimplements this algorithm, with the the additional benefit of increased interoperability with standard data structures and modeling ecosystems.

Last updated 4 months ago

3.85 score 5 scripts

amplify - Automate PCR Tasks Reproducibly

PCR tasks - like plate layout planning, dilution calculations, visualization, and analysis - are often repetitive, tedious, prone to error, and poorly documented. amplify seeks to automate these tasks, as well as documenting them (through both code and generated reports) as a bonus.

Last updated 2 months ago

3.78 score 4 scripts

blotbench - Easy, reproducible Westen blot editing

blotbench includes a rudimentary visual image editor that helps you write reproducible, declarative, auditable code for editing western blots. Additionally, it provides tools for easily producing annotated, publication-ready images quickly.

Last updated 11 months ago

3.78 score 2 stars 2 scripts