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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

cancer-genomicstidy

5.56 score 19 stars 33 scripts 1.2k 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.

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ggplot2

4.60 score 4 stars 3 dependents 11 scripts

mop - A 'broom'-like Interface to Lab Data

What the package does (one paragraph).

Last updated

3.10 score 1 stars 3 dependents 28 scripts 629 downloads

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.

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2.70 score 1 stars 2 scripts

qp - A toolkit for analyzing protein quantification results

What the package does (one paragraph).

Last updated

2.70 score 8 scripts 28 downloads

ezmtt - Easy MTT Assay Tidying and Plotting

This package automates the analysis and plotting of standard MTT workflows.

Last updated

2.70 score 3 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

1.70 score 5 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.

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1.70 score 7 scripts

thermos - Interface with IonReporter from R

thermos allows you to use the IonReporter API with R

Last updated

1.70 score

classifyBLCA - What the Package Does (One Line, Title Case)

What the package does (one paragraph).

Last updated

1.70 score