Package: apComplex 2.73.0

Denise Scholtens

apComplex: Estimate protein complex membership using AP-MS protein data

Functions to estimate a bipartite graph of protein complex membership using AP-MS data.

Authors:Denise Scholtens <[email protected]>

# Install 'apComplex' in R:

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

Datasets:

HMSPCI - High-Throughput Mass Spectromic Protein Complex Identification
HMSPCIgraph - High-Throughput Mass Spectromic Protein Complex Identification
Krogan - High-Definition Macromolecular Composition of Yeast RNA-Processing Complexes
MBMEcHMSPCI - HMSPCI data complex estimates
MBMEcKrogan - Krogan data complex estimates
MBMEcTAP - TAP data complex estimates
SBMHcHMSPCI - HMSPCI data complex estimates
SBMHcTAP - TAP data complex estimates
TAP - Tandem Affinity Purification
TAPgraph - Tandem Affinity Purification
UnRBBcHMSPCI - HMSPCI data complex estimates
UnRBBcTAP - TAP data complex estimates
apEX - Example data set for apComplex package
apEXG - Example data set for apComplex package
gavin06FilteredEstimates - AP-MS data complex estimates
gavinBP2006 - Tandem Affinity Purification
krogan06FilteredEstimates - AP-MS data complex estimates
kroganBPMat2006 - Tandem Affinity Purification
yNameTAP - TAP data complex estimates using standard gene names
yTAP - YTAP Complexes published Gavin, et al. (2002).

On BioConductor:apComplex-2.73.0(bioc 3.21)apComplex-2.72.0(bioc 3.20)

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

Last updated 2 months agofrom:f895ff93a7. Checks:OK: 1 NOTE: 6. Indexed: yes.

Last update: 2013-11-01
Started: 2013-11-01

Help page	Topics
AP-MS data complex estimates	gavin06FilteredEstimates krogan06FilteredEstimates
Example data set for apComplex package	apEX apEXG
Find maximal BH-complete subgraph	bhmaxSubgraph
Estimate a Protein Complex Membership Graph (PCMG) using protein complex comembership data from AP-MS technology	findComplexes
Tandem Affinity Purification (TAP) Data from Gavin et al. (2006)	gavinBP2006 gavinBP2006graph
High-Throughput Mass Spectromic Protein Complex Identification (HMS-PCI) Data from Ho, et al. (2002)	HMSPCI HMSPCIgraph
HMSPCI data complex estimates	MBMEcHMSPCI SBMHcHMSPCI UnRBBcHMSPCI
High-Definition Macromolecular Composition of Yeast RNA-Processing Complexes (2004)	Krogan
Krogan data complex estimates	MBMEcKrogan
Tandem Affinity Purification (TAP) Data from Krogan et al. (2006)	kroganBPMat2006
Computes change in LxC measure	adjBinFUN fisherFUN LCjoin LCjoinadjBin LCjoinfisher LCjoinLchange
Iteratively combine columns in initial PCMG estimate	mergeComplexes
Render complex estimates	plotComplex
Sort complex estimates	sortComplexes
Tandem Affinity Purification (TAP) Data from Gavin et al. (2002)	TAP TAPgraph
TAP data complex estimates	MBMEcTAP SBMHcTAP UnRBBcTAP
TAP data complex estimates using standard gene names	yNameTAP
yTAP Complexes published Gavin, et al. (2002).	yTAP