Package: creedenzymatic 6.1.0

Ali Sajid Imami

creedenzymatic: creedenzymatic

Combine kinome results from KRSA and UKA and other tools A package for integrating upstream kinases analyses

Authors:Ali Sajid Imami [aut, cre], Khaled Alganem [aut], Justin Creeden [aut], Abdul-Rizaq Hamoud [aut]

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|manual.html✨
DESCRIPTION
card.svg |card.png
creedenzymatic/json (API)

# Install 'creedenzymatic' in R:

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

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

Datasets:

kinome_mp_file - CDRL Complete mapping file
kinome_mp_file_v1 - CDRL Complete mapping file
kinome_mp_file_v2 - CDRL Complete mapping file
kinome_mp_file_v3 - CDRL Complete mapping file
kinome_mp_file_v4 - CDRL Complete mapping file
ptk_pamchip_86402_array_layout_ptmsea - CDRL Complete mapping of peptides - used for ptm-sea
ptk_pamchip_86402_mapping - CDRL Complete mapping of peptides to HGNC symbols
stk_pamchip_87102_array_layout_ptmsea - CDRL Complete mapping of peptides - used for ptm-sea
stk_pamchip_87102_mapping - CDRL Complete mapping of peptides to HGNC symbols
uka_db_full - UKA Complete DB mapping File

On CRAN:

bioconductor bioconductor-package kinome

3.45 score 1 stars 28 scripts 37 exports 61 dependencies

Last updated from:f8bb066c21. Checks:7 WARNING, 1 ERROR, 1 OK. Indexed: yes.

Target	Result	Time
linux-devel-x86_64	WARNING	161
source / vignettes	ERROR	250
linux-release-x86_64	WARNING	151
macos-release-arm64	WARNING	89
macos-oldrel-arm64	WARNING	85
windows-devel	WARNING	98
windows-release	WARNING	106
windows-oldrel	WARNING	98
wasm-release	OK	116

Exports:.align_matrices .check_colnames .check_dups .extract.gct .is.wholenumber .na_pad_matrix .parse.gctx .parse.gmt .parse.gmx .parse.grp .read.gctx.ids .read.gctx.meta .update.gctx .write.gct .write.gctx .write.gmt .write.grp .write.tbl %>%annotate.gct combine_tools creedenzymatic extract_top_kinases melt.gct merge.gct quartile_figure rank_kinases rank.gct read_kea read_krsa read_ptmsea read_uka run_kea run_ptmsea ssGSEA2_ce subset.gct transpose.gct

Dependencies:askpass bit bit64 boot CircStats cli clipr codetools cpp11 crayon curl dotCall64 dplyr dtw farver fields foreach generics ggplot2 glue gtable gtools hms httr isoband iterators jsonlite labeling lifecycle magrittr maps MASS mime openssl pillar pkgconfig prettyunits progress proxy purrr R6 RColorBrewer Rcpp readr rlang S7 scales spam stringi stringr sys tibble tidyr tidyselect tzdb utf8 vctrs verification viridisLite vroom withr

Vignettes and/or manual for this package failed to build, some documents may be unavailable. Please inspect thebuild logs for more information.

creedenzymatic

Rendered fromcreedenzymatic.Rmdusingknitr::rmarkdown

Last update: 2021-11-16
Started: 2021-05-12

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Align the rows and columns of two (or more) matrices	.align_matrices
Check whether 'test_names' are columns in the 'data.frame' df	.check_colnames
Check for duplicates in a vector	.check_dups
Exract elements from a GCT matrix	.extract.gct
Check if x is a whole number	.is.wholenumber
Pad a matrix with additional rows/columns of NA values	.na_pad_matrix
Parse a GCTX file into the workspace as a GCT object	.parse.gctx
Read a GMT file and return a list	.parse.gmt
Read a GMX file and return a list	.parse.gmx
Read a GRP file and return a vector of its contents	.parse.grp
Read GCTX row or column ids	.read.gctx.ids
Parse row or column metadata from GCTX files	.read.gctx.meta
Update the matrix of an existing GCTX file	.update.gctx
Write a GCT object to disk in GCT format	.write.gct
Write a GCT object to disk in GCTX format	.write.gctx
Write a nested list to a GMT file	.write.gmt
Write a vector to a GRP file	.write.grp
Write a 'data.frame' to a tab-delimited text file	.write.tbl
Add annotations to a GCT object	annotate.gct
Combine data for quartile figure	combine_tools
Runs Creedenzymatic	creedenzymatic
Extract Top Kinases	extract_top_kinases
An S4 class to represent a GCT object	GCT-class
CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA)	kinome_mp_file
CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA)	kinome_mp_file_v1
CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA)	kinome_mp_file_v2
CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA)	kinome_mp_file_v3
CDRL Complete mapping file (UKA+KRSA+KEA3+PTM-SEA)	kinome_mp_file_v4
Transform a GCT object in to a long form 'data.table' (aka 'melt')	melt.gct
Merge two GCT objects together	merge.gct
CDRL Complete mapping of peptides - used for ptm-sea (PTK PamChip 86402)	ptk_pamchip_86402_array_layout_ptmsea
CDRL Complete mapping of peptides to HGNC symbols (PTK PamChip 86402)	ptk_pamchip_86402_mapping
Plot quartile Figure	quartile_figure
Rank Kinases based on a score	rank_kinases
Convert a GCT object's matrix to ranks	rank.gct
Reads a dataframe of Peptides IDs and their Scores and run KEA3	read_kea
Reads and Rank KRSA table	read_krsa
Reads a dataframe of Peptides IDs and their Scores and run PTM-SEA	read_ptmsea
Reads and Rank UKA table	read_uka
Run KEA3 API based on a set of gene symbols	run_kea
Run PTM-SEA API using a gct file as input	run_ptmsea
CDRL Complete mapping of peptides - used for ptm-sea (STK PamChip 87102)	stk_pamchip_87102_array_layout_ptmsea
CDRL Complete mapping of peptides to HGNC symbols (STK PamChip 87102)	stk_pamchip_87102_mapping
Subset a gct object using the provided row and column ids	subset.gct
Transpose a GCT object	transpose.gct
UKA Complete DB mapping File (STK + PTK)	uka_db_full