Package: TSAR 1.11.0

Xinlin Gao

TSAR: Thermal Shift Analysis in R

This package automates analysis workflow for Thermal Shift Analysis (TSA) data. Processing, analyzing, and visualizing data through both shiny applications and command lines. Package aims to simplify data analysis and offer front to end workflow, from raw data to multiple trial analysis.

Authors:Xinlin Gao [aut, cre], William M. McFadden [aut, fnd], Zhijiang Ye Ye [aut, fnd], Stefan G. Sarafianos [fnd, aut, ths]

TSAR_1.11.0.tar.gz
TSAR_1.11.0.zip(r-4.7)TSAR_1.11.0.zip(r-4.6)TSAR_1.11.0.zip(r-4.5)
TSAR_1.11.0.tgz(r-4.6-any)TSAR_1.11.0.tgz(r-4.5-any)
TSAR_1.11.0.tar.gz(r-4.7-any)TSAR_1.11.0.tar.gz(r-4.6-any)
TSAR_1.11.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
TSAR/json (API)
NEWS

# Install 'TSAR' in R:

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

Datasets:

example_normalized_data - Example normalized TSA dataset
example_tsar_data - Example tsar_data file
qPCR_data1 - QPCR_data1 Dataset
qPCR_data2 - QPCR_data2 Dataset
well_information - Example well information Data
well_information_template - Well Information Template

On BioConductor:TSAR-1.11.0(bioc 3.24)TSAR-1.10.0(bioc 3.23)

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

software shinyapps visualization qpcr

5.23 score 14 scripts 258 downloads 35 exports 129 dependencies

Last updated from:5ead14fb1d. Checks:1 ERROR, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	ERROR	200
linux-devel-x86_64	NOTE	278
source / vignettes	OK	257
linux-release-x86_64	NOTE	265
macos-release-arm64	NOTE	134
macos-oldrel-arm64	NOTE	148
windows-devel	NOTE	179
windows-release	NOTE	175
windows-oldrel	NOTE	179
wasm-release	OK	147

Exports:analyze_norm condition_IDs gam_analysis get_legend graph_tsar join_well_info merge_norm merge_TSA model_beta model_boltzmann model_fit model_gam normalize normalize_fluorescence read_analysis read_raw_data read_tsar remove_raw rescale run_boltzmann screen Tm_difference Tm_est TSA_average TSA_boxplot TSA_compare_plot TSA_ligands TSA_proteins TSA_Tms TSA_wells_plot view_deriv view_model weed_raw well_IDs write_tsar

Dependencies:abind askpass backports base64enc boot broom bslib cachem car carData cellranger cli colorspace commonmark corrplot cowplot cpp11 crayon crosstalk curl data.table Deriv digest doBy dplyr evaluate farver fastmap fontawesome forecast Formula fracdiff fs generics ggplot2 ggpubr ggrepel ggsci ggsignif glue gridExtra gtable highr hms htmltools htmlwidgets httpuv httr isoband jquerylib jsonlite knitr labeling later lattice lazyeval lifecycle lme4 lmtest magrittr MASS Matrix MatrixModels memoise mgcv microbenchmark mime minpack.lm minqa modelr nlme nloptr nnet numDeriv openssl openxlsx otel pbkrtest pillar pkgconfig plotly polynom prettyunits progress promises purrr quantreg R6 rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen Rdpack readxl reformulas rematch rhandsontable rlang rmarkdown rstatix S7 sass scales shiny shinyjs shinyWidgets sourcetools SparseM stringi stringr survival sys tibble tidyr tidyselect timeDate tinytex urca utf8 vctrs viridisLite withr xfun xtable yaml zip zoo

Frequently Asked Questions

Rendered fromFAQ_assistance.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2024-04-06
Started: 2023-08-08

TSAR Package Structure

Rendered fromTSAR_Package_Structure.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-12-19
Started: 2023-06-23

TSAR Workflow by Command

Rendered fromTSAR_Workflow_by_Command.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-12-19
Started: 2023-07-05

TSAR Workflow by Shiny

Rendered fromTSAR_Workflow_by_Shiny.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2025-12-15
Started: 2023-07-05

Help page	Topics
Analyze to Normalize	analyze_norm
TSAR Condition IDs	condition_IDs
Example normalized TSA dataset	example_normalized_data
Example tsar_data file	example_tsar_data
Analysis of all 96 wells through gam modeling	gam_analysis
Extract ggplot2 legend	get_legend
Graph tsar_data	graph_tsar
Well information input function	join_well_info
Merge and format norm_data into tsar_data	merge_norm
Merge TSA Raw Data and Analysis Files	merge_TSA
Beta-knot natural cubic spline model (Tm-centered via numerical_Tm)	model_beta
Boltzmann Modeling on TSA data	model_boltzmann
Refit and calculate derivative function	model_fit
Generalized Addidtive Modeling on TSA data	model_gam
Normalize Fluorescence	normalize
Normalize Fluorescence Curve	normalize_fluorescence
Numerical Tm by treating Tm as inflection point	numerical_Tm
qPCR_data1 Dataset	qPCR_data1
qPCR_data2 Dataset	qPCR_data2
Read TSA Analysis Data	read_analysis
Read TSA Raw Data	read_raw_data
Read analysis result	read_tsar
Remove selected raw curves	remove_raw
Rescale values between minimum and maximum.	rescale
Run Boltzmann Modeling	run_boltzmann
Screen raw curves	screen
Calculate Tm difference for all conditions	Tm_difference
Find inflection point function	Tm_est
Average TSA Curves	TSA_average
TSA Box Plot	TSA_boxplot
Compare TSA curves to control	TSA_compare_plot
TSA Ligands	TSA_ligands
TSA Proteins	TSA_proteins
Diagnose Smoother Accuracy Across Conditions	TSA_smoother_diagnostics
Reformat TSA data into TSA Tms	TSA_Tms
TSA Well Curves Plot	TSA_wells_plot
View Derivative Curves	view_deriv
View Model	view_model
Weed raw data for corrupt curves	weed_raw
TSAR Well IDs	well_IDs
example well information Data	well_information
Well Information Template	well_information_template
write output files	write_tsar

Package: TSAR 1.11.0

TSAR: Thermal Shift Analysis in R

Frequently Asked Questions

TSAR Package Structure

TSAR Workflow by Command

TSAR Workflow by Shiny

Citation

Development and contributors

Readme and manuals

Help Manual

Usage by other packages (reverse dependencies)