Package: InflectSSP 1.6

Amber Mosley

InflectSSP: Melt Curve Fitting and Melt Shift Analysis

Analyzes raw abundance data from a cellular thermal shift experiment and calculates melt temperatures and melt shifts for each protein in the experiment. McCracken (2022) <doi:10.1101/2022.12.30.522131>.

Authors:Neil McCracken [aut], Hao Liu [ctb], Amber Mosley [cre]

InflectSSP_1.6.tar.gz
InflectSSP_1.6.tar.gz(r-4.5-noble)InflectSSP_1.6.tar.gz(r-4.4-noble)
InflectSSP_1.6.tgz(r-4.4-emscripten)InflectSSP_1.6.tgz(r-4.3-emscripten)
InflectSSP.pdf |InflectSSP.html✨
InflectSSP/json (API)

# Install 'InflectSSP' in R:

install.packages('InflectSSP', repos = c('https://cran.r-universe.dev', 'https://cloud.r-project.org'))

Uses libs:

openjdk– OpenJDK Java runtime, using Hotspot JIT

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

2.00 score 3 scripts 747 downloads 10 exports 66 dependencies

Last updated 2 years agofrom:633aaba14d. Checks:OK: 1 NOTE: 1. Indexed: yes.

Target	Result	Date
Doc / Vignettes	OK	Nov 01 2024
R-4.5-linux	NOTE	Nov 01 2024

Exports:Correction CurveFit1 CurveFit2 Import InflectSSP MeltCalc Normalize Quantify ReportDataMelts ReportSTRING

Dependencies:askpass cellranger cli coda colorspace cpp11 crayon curl data.table dplyr fansi farver forcats generics GGally ggplot2 ggstats glue gtable hms httr isoband jsonlite labeling lattice lifecycle magrittr MASS Matrix mgcv mime munsell network nlme openssl patchwork pillar pkgconfig plotrix plyr prettyunits progress purrr R6 RColorBrewer Rcpp readxl rematch rJava rlang scales statnet.common stringi stringr svglite sys systemfonts tibble tidyr tidyselect utf8 vctrs viridisLite withr xlsx xlsxjars

InflectSSPVignette

Neil McCracken

Rendered fromInflectSSPVignette.Rmdusingknitr::rmarkdownon Nov 01 2024.

Last update: 2023-02-03
Started: 2021-12-16

Citation

Readme and manuals

Help Manual

Help page	Topics
This function corrects the normalized abundance of each protein using a correction constant that is calculated in this function. The correction constant is determined using the difference between actual and predicted fit at the proteome level.	Correction
This function determines the 4 parameter or 3 parameter log fit for the proteome level curve.	CurveFit1
This function determines the best curve fit for each protein using the data post correction and also determines the R squared for each curve fit	CurveFit2
This function imports data that will be analyzed in downstream functions.	Import
This function is the primary function that calls other functions in the program.	InflectSSP
This function determines melt shifts for all proteins that meet quality criteria and also determines the melt shift p-values	MeltCalc
This function normalizes the abundance values to that measured at the lowest temperature	Normalize
This function determines the median abundance value across the proteome for all experiments together	Quantify
This function generates results from the Inflect function after applying criteria input from the user	ReportDataMelts
This function generates a STRING based network using the significant melt shifts from analysis	ReportSTRING