Package: KRSA 1.99.42

Ali Sajid Imami

KRSA: KRSA: Kinome Random Sampling Analyzer

The goal of this package is to analyze the PamChip data and identify the changes in the active kinome. The package can preprocess the PamChip data output from BioNavigator and use Random Sampling and Permutation Analysis to identify upstream kinases. Additionally, this package provides a set of useful visualizations for the PamChip data.

Authors:Ali Sajid Imami [aut, cre], Khaled Alganem [aut]

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 |KRSA.html✨
KRSA/json (API)

# Install 'KRSA' in R:
install.packages('KRSA', repos = c('https://cogdisreslab.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/cogdisreslab/krsa/issues

Datasets:

On CRAN:

kinasephosphatasespamchipkinomerandom samplingpermutation analysis

4.20 score 4 stars 47 scripts 35 exports 60 dependencies

Last updated 2 days agofrom:df3f9da13c. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILNov 20 2024
R-4.5-winWARNINGNov 20 2024
R-4.5-linuxWARNINGNov 20 2024
R-4.4-winWARNINGNov 20 2024
R-4.4-macWARNINGNov 20 2024
R-4.3-winWARNINGNov 20 2024
R-4.3-macWARNINGNov 20 2024

Exports:%>%enrichr_lib_callkrsakrsa_ball_modelkrsa_ce_output_kinaseskrsa_ce_output_peptideskrsa_coverage_plotkrsa_curve_plotkrsa_cv_plotkrsa_enrichrkrsa_enrichr_plotkrsa_extractEndPointkrsa_extractEndPointMaxExpkrsa_filter_lowPepskrsa_filter_nonLinearkrsa_filter_ref_pepkrsa_get_diffkrsa_get_diff_byChipkrsa_group_diffkrsa_heatmapkrsa_heatmap_groupedkrsa_histogram_plotkrsa_qc_stepskrsa_quick_filterkrsa_readkrsa_reverse_krsa_plotkrsa_samplingkrsa_scaleModelkrsa_show_peptideskrsa_top_hitskrsa_violin_plotkrsa_violin_plot_groupedkrsa_waterfallkrsa_zscores_plotparse_BN_crosstabFile

Dependencies:askpassbackportsbitbit64broomclicliprcolorspacecpp11crayoncurldplyrEnvStatsfansifarvergenericsggplot2ggsignifgluegtablehmshttrigraphisobandjsonlitelabelinglatticelifecyclemagrittrMASSMatrixmgcvmimemunsellnlmenortestopensslpheatmappillarpkgconfigprettyunitsprogresspurrrR6RColorBrewerreadrrlangscalesstringistringrsystibbletidyrtidyselecttzdbutf8vctrsviridisLitevroomwithr

Readme and manuals

Help Manual

Help pageTopics
Protein-Protein Interactions based on PhosphositePlus databaseballModel_edges
Protein-Protein Interactions based on PhosphositePlus databaseballModel_nodes
Runs enrichr api (single GET call for a geneset library)enrichr_lib_call
Main KRSA function. It performs the random sampling analysis and generates a Z score table and a count matrixkrsa
Generates a kinase ball model using the Z score tablekrsa_ball_model
It prepares a KRSA kinase file to be used for creedenzymatickrsa_ce_output_kinases
It prepares a KRSA peptide file (log2 FC) to be used for creedenzymatickrsa_ce_output_peptides
Generates a coverage plot (Percentage of total coverage of kinases on chip)krsa_coverage_plot
KRSA kinase coverage file for PamChip 86402 PTK (v1 mapping)KRSA_coverage_PTK_PamChip_86402_v1
KRSA kinase coverage file for PamChip 87102 STK (v1 mapping)KRSA_coverage_STK_PamChip_87102_v1
KRSA kinase coverage file for PamChip 87102 STK (v2 mapping, removed PDK kinase)KRSA_coverage_STK_PamChip_87102_v2
Generates curves plots per peptide using the last cycle datakrsa_curve_plot
Generates CV (coefficient of variation) plotkrsa_cv_plot
Runs enrichr analysis using a list of PamChip peptide IDs or geneskrsa_enrichr
Visualize the enrichr analysiskrsa_enrichr_plot
Extracts end point data (last cycle)krsa_extractEndPoint
Extracts end point data at max exposure (last cycle)krsa_extractEndPointMaxExp
Filters out peptides with low signals based on the pw data (max exposure)krsa_filter_lowPeps
Filters out peptides with none linear signals based on the pw datakrsa_filter_nonLinear
Filters out ref peptideskrsa_filter_ref_pep
Extract differential peptides based on LFC cutoffkrsa_get_diff
Extract differential peptides based on LFC cutoff by chip/barcodekrsa_get_diff_byChip
Calculates LFC based on modeled pw data and groupingkrsa_group_diff
Generates a heatmap based on the modeled pw datakrsa_heatmap
Generates a grouped heatmapkrsa_heatmap_grouped
Generates kinase histogram plots based on the KRSA function outputkrsa_histogram_plot
KRSA kinase-substrate mapping file for PamChip 86402 PTK (v1 mapping)KRSA_Mapping_PTK_PamChip_86402_v1
KRSA kinase-substrate mapping file for PamChip 87102 STK (v1 mapping)KRSA_Mapping_STK_PamChip_87102_v1
QC pre-processing of raw data (deals with negative values, and adjust signal saturation values)krsa_qc_steps
Filters out low signal peptides AND none linear peptideskrsa_quick_filter
Read crosstab format files exported from bioNavigator and tidy themkrsa_read
Generates the reverse krsa plot (to examine kinase activity)krsa_reverse_krsa_plot
Performs random sampling of peptides and mapped kinaseskrsa_sampling
Fits, scales, transforms, and normalize kinome array datakrsa_scaleModel
Determine number of peptides inside listskrsa_show_peptides
Extracts top kinase hits based on a Z cutoffkrsa_top_hits
Generates violin plots based on peptides signals intensitieskrsa_violin_plot
Generates grouped violin plots based on peptides signals intensities with t tests optionskrsa_violin_plot_grouped
Generates a waterfall figure based on the LFC tablekrsa_waterfall
Generates a waterfall figure based on the Z score tablekrsa_zscores_plot
Parse bionavigator crosstab filesparse_BN_crosstabFile
CDRL Complete mapping of peptides to HGNC symbols (PTK PamChip 86402)ptk_pamchip_86402_mapping
CDRL Complete mapping of peptides to HGNC symbols (STK PamChip 87102)stk_pamchip_87102_mapping