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bartongroup
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Proteus
R package for analysing proteomics data
MIT License
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Differences in proteusData when using readProteinGroups with different conditions
#49
WackerO
opened
1 year ago
0
fetchFromUniProt error
#48
tfccheng
opened
1 year ago
1
Not compatible with R version
#47
cstgermain4
closed
1 year ago
1
Add proteus to bioconda
#46
WackerO
opened
1 year ago
3
Error in limmaRatioDE function
#45
TaraBartolec
closed
2 years ago
1
extract peptide/protein count
#44
francescocay
closed
3 years ago
1
How to make protein table?
#43
yueli8
opened
3 years ago
0
Error in normalizeData(LH) : Input data must be of class proteusData.
#42
yueli8
opened
4 years ago
0
Normalize the data of SILAC
#41
yueli8
closed
4 years ago
2
How to integrate Phospho (STY)Sites.txt into Proteus analysis?
#40
subwaystation
opened
4 years ago
0
Saving plotFID_live and plotVolcano_live
#39
zillurbmb51
opened
4 years ago
2
About library
#38
ypriverol
closed
4 years ago
1
Normalization with different number of samples in experiments
#37
PolinaLip
opened
4 years ago
0
Create LICENSE
#36
MarekGierlinski
closed
4 years ago
0
Function readEvidenceFile doesn't work
#35
sago91
closed
4 years ago
2
Setting different measure.cols for readProteinGroups
#34
cmysrobinso
closed
4 years ago
2
PCA function missing
#33
gurpreet-bioinfo
closed
4 years ago
3
Error in the extraction commands while retrieving ids
#32
gurpreet-bioinfo
closed
4 years ago
3
Reduced number of entries from readProteinsGroups
#31
gurpreet-bioinfo
closed
4 years ago
2
Vignettes do not install
#30
MarekGierlinski
closed
5 years ago
1
Replicates in the same mix?
#29
evertonjlima
closed
4 years ago
1
Error with makePeptideTable(evi, meta), Intensity not found
#28
Sabbalonn
closed
5 years ago
1
Problem with parallel::mclapply on Windows
#27
Pam65
closed
5 years ago
3
Spike-in SILAC?
#26
vidaletal
closed
5 years ago
1
Vignettes not installing?
#25
ar3781
closed
5 years ago
1
Issues with phantom condition levels
#24
MarekGierlinski
closed
5 years ago
1
PlotVolcano live condition (x-axis) label text
#23
ygyue
closed
5 years ago
3
Reference and PRIDE dataset in TMT vignette are incorrect
#22
pwilmart
closed
6 years ago
2
allowedUniprotColumns not exported
#21
MarekGierlinski
closed
6 years ago
1
makeProteinTable crashes with one condition
#20
MarekGierlinski
closed
6 years ago
1
Ngood in limmaDE should only contain two conditions
#19
MarekGierlinski
closed
6 years ago
1
min.peptides should be 2 by default
#18
MarekGierlinski
closed
6 years ago
1
Gene names needed
#17
MarekGierlinski
closed
4 years ago
0
Libraries required
#16
MarekGierlinski
closed
6 years ago
1
Crash when evidence without "Experiment" column provided
#15
MarekGierlinski
closed
6 years ago
1
plotVolcano_life produces error message with peptide data
#14
MarekGierlinski
closed
6 years ago
1
no heatmaps in live.R functions
#13
Gasta88
closed
6 years ago
1
Non-unique annotations
#12
MarekGierlinski
closed
6 years ago
1
Annotation on R/live.R
#11
Gasta88
closed
6 years ago
0
Correction for the *_live features
#10
Gasta88
closed
6 years ago
0
R/live.R and relative docs
#9
Gasta88
closed
6 years ago
0
limma result: first column is always "protein"
#8
MarekGierlinski
closed
6 years ago
1
pep2prot table in peptides contains NAs
#7
MarekGierlinski
closed
6 years ago
1
Dealing with peptides/proteins that aren't detected in all conditions...
#6
nickschurch
closed
6 years ago
2
significance threshold set in limmaDE
#5
nickschurch
closed
7 years ago
2
Choosing p-value column for volcano plot...
#4
nickschurch
closed
6 years ago
1
Make log transform for limmaDE a parameter and set default to log2
#3
nickschurch
closed
6 years ago
3
plotPeptideCount labels y-axis as 'peptide' even with protein table
#2
nickschurch
closed
7 years ago
1
Vignette doesn't import 'parallel'
#1
nickschurch
closed
7 years ago
1