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NGCHM - Next Generation Clustered Heat Maps

Next-Generation Clustered Heat Maps (NG-CHMs) allow for dynamic exploration of heat map data in a web browser. 'NGCHM' allows users to create both stand-alone HTML files containing a Next-Generation Clustered Heat Map, and .ngchm files to view in the NG-CHM viewer. See Ryan MC, Stucky M, et al (2020) <doi:10.12688/f1000research.20590.2> for more details.

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heatmapnci-itcrng-chm

4.64 score 9 stars 32 scripts 644 downloads

RPPASPACE - Reverse-Phase Protein Array Super Position and Concentration Evaluation

Provides tools for the analysis of reverse-phase protein arrays (RPPAs), which are also known as 'tissue lysate arrays' or simply 'lysate arrays'. The package's primary purpose is to input a set of quantification files representing dilution series of samples and control points taken from scanned RPPA slides and determine a relative log concentration value for each valid dilution series present in each slide and provide graphical visualization of the input and output data and their relationships. Other optional features include generation of quality control scores for judging the quality of the input data, spatial adjustment of sample points based on controls added to the slides, and various types of normalization of calculated values across a set of slides. The package was derived from a previous package named SuperCurve. For a detailed description of data inputs and outputs, usage information, and a list of related papers describing methods used in the package please review the vignette 'Guide_to_RPPASPACE'. 'RPPA SPACE: an R package for normalization and quantitation of Reverse-Phase Protein Array data'. Bioinformatics Nov 15;38(22):5131-5133. <doi: 10.1093/bioinformatics/btac665>.

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4.18 score 3 stars 224 downloads

tsvio - Simple Utilities for Tab-Separated-Value (TSV) Files

Utilities for rapidly loading specified rows and/or columns of data from large tab-separated value (tsv) files (large: e.g. 1 GB file of 10000 x 10000 matrix). 'tsvio' is an R wrapper to 'C' code that creates an index file for the rows of the tsv file, and uses that index file to collect rows and/or columns from the tsv file without reading the whole file into memory.

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4.18 score 1 stars 1 dependents 8 scripts 698 downloads

NGCHMSupportFiles - Support Files for Building Next Generation Clustered Heat Maps (NG-CHMs)

Support files required by the 'NGCHM' package to export Next-Generation Clustered Heat Maps (NG-CHMs) to .ngchm, HTML, and PDF files. These support files are updated mostly independently from the 'NGCHM' package, and are therefore provided separately.

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2.00 score 20 scripts

NGCHMDemoData - Demo Data for the NGCHM R Package

Package of demo data for NGCHM vignettes.

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1.93 score 17 scripts