Estimating Absolute Protein Quantities from Label-Free LC-MS/MS Proteomics Data

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Documentation for package ‘aLFQ’ version 1.3.6

• DESCRIPTION file.

Help Pages

aLFQ-package	aLFQ
AbsoluteQuantification	Absolute label-free quantification of mass spectrometry proteomics experiments
AbsoluteQuantification.default	Absolute label-free quantification of mass spectrometry proteomics experiments
ALF	Generate ALF report
ALF.default	Generate ALF report
aLFQ	aLFQ
APEX	Training, testing and validation of APEX peptide observability models
APEX.default	Training, testing and validation of APEX peptide observability models
apexFeatures	Calculation of physicochemical amino acid properties for APEX
apexFeatures.default	Calculation of physicochemical amino acid properties for APEX
APEXMS	Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
APEX_LCQ	Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
APEX_ORBI	Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
cval	Absolute label-free quantification of mass spectrometry proteomics experiments
cval.AbsoluteQuantification	Absolute label-free quantification of mass spectrometry proteomics experiments
cval.APEX	Training, testing and validation of APEX peptide observability models
cval.default	Absolute label-free quantification of mass spectrometry proteomics experiments
export	Absolute label-free quantification of mass spectrometry proteomics experiments
export.AbsoluteQuantification	Absolute label-free quantification of mass spectrometry proteomics experiments
export.default	Absolute label-free quantification of mass spectrometry proteomics experiments
hist.AbsoluteQuantification	Absolute label-free quantification of mass spectrometry proteomics experiments
import	import of mass spectrometry proteomics data analysis software reports.
import.default	import of mass spectrometry proteomics data analysis software reports.
LUDWIGMS	Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry..
LUDWIG_SRM	Estimation of Absolute Protein Quantities of Unlabeled Samples by Selected Reaction Monitoring Mass Spectrometry..
PeptideInference	Peptide inference for aLFQ import data frame
PeptideInference.default	Peptide inference for aLFQ import data frame
pivot	Absolute label-free quantification of mass spectrometry proteomics experiments
pivot.AbsoluteQuantification	Absolute label-free quantification of mass spectrometry proteomics experiments
pivot.default	Absolute label-free quantification of mass spectrometry proteomics experiments
plot.AbsoluteQuantification	Absolute label-free quantification of mass spectrometry proteomics experiments
plot.APEX	Training, testing and validation of APEX peptide observability models
predict.AbsoluteQuantification	Absolute label-free quantification of mass spectrometry proteomics experiments
predict.APEX	Training, testing and validation of APEX peptide observability models
print.AbsoluteQuantification	Absolute label-free quantification of mass spectrometry proteomics experiments
print.APEX	Training, testing and validation of APEX peptide observability models
print.apexFeatures	Calculation of physicochemical amino acid properties for APEX
ProteinInference	Protein inference for aLFQ import data frame
ProteinInference.default	Protein inference for aLFQ import data frame
proteotypic	Prediction of the flyability of proteotypic peptides
proteotypic.default	Prediction of the flyability of proteotypic peptides
UPS2	Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
UPS2MS	Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
UPS2_LFQ	Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
UPS2_SC	Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.
UPS2_SRM	Calculating absolute and relative protein abundance from mass spectrometry-based protein expression data.