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

Peer review:

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

Datasets:

On CRAN:

bioconductorbioconductor-packagekinome

3.60 score 1 stars 20 scripts 37 exports 67 dependencies

Last updated 9 months agofrom:f8bb066c21. Checks:ERROR: 1 WARNING: 6. Indexed: yes.

TargetResultDate
Doc / VignettesFAILDec 25 2024
R-4.5-winWARNINGDec 25 2024
R-4.5-linuxWARNINGDec 25 2024
R-4.4-winWARNINGDec 25 2024
R-4.4-macWARNINGDec 25 2024
R-4.3-winWARNINGDec 25 2024
R-4.3-macWARNINGDec 25 2024

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.gctcombine_toolscreedenzymaticextract_top_kinasesmelt.gctmerge.gctquartile_figurerank_kinasesrank.gctread_kearead_krsaread_ptmsearead_ukarun_kearun_ptmseassGSEA2_cesubset.gcttranspose.gct

Dependencies:askpassbitbit64bootCircStatsclicliprcodetoolscolorspacecpp11crayoncurldotCall64dplyrdtwfansifarverfieldsforeachgenericsggplot2gluegtablegtoolshmshttrisobanditeratorsjsonlitelabelinglatticelifecyclemagrittrmapsMASSMatrixmgcvmimemunsellnlmeopensslpillarpkgconfigprettyunitsprogressproxypurrrR6RColorBrewerRcppreadrrlangscalesspamstringistringrsystibbletidyrtidyselecttzdbutf8vctrsverificationviridisLitevroomwithr

creedenzymatic

Rendered fromcreedenzymatic.Rmdusingknitr::rmarkdownon Dec 25 2024.

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

Readme and manuals

Help Manual

Help pageTopics
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 objectannotate.gct
Combine data for quartile figurecombine_tools
Runs Creedenzymaticcreedenzymatic
Extract Top Kinasesextract_top_kinases
An S4 class to represent a GCT objectGCT-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 togethermerge.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 Figurequartile_figure
Rank Kinases based on a scorerank_kinases
Convert a GCT object's matrix to ranksrank.gct
Reads a dataframe of Peptides IDs and their Scores and run KEA3read_kea
Reads and Rank KRSA tableread_krsa
Reads a dataframe of Peptides IDs and their Scores and run PTM-SEAread_ptmsea
Reads and Rank UKA tableread_uka
Run KEA3 API based on a set of gene symbolsrun_kea
Run PTM-SEA API using a gct file as inputrun_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 idssubset.gct
Transpose a GCT objecttranspose.gct
UKA Complete DB mapping File (STK + PTK)uka_db_full