ComputationalProteomics/NormalyzerDE issues and pull requests

#40 - Categorical anova used when analyzing normalizations directly

Pull Request - State: closed - Opened by Jakob37 6 months ago

#39 - Deprecation warning in ggplot, and remove unneeded dependency

Pull Request - State: closed - Opened by Jakob37 6 months ago

#38 - Exporting relevant intragroup variations functions

Issue - State: closed - Opened by lisiarend 7 months ago - 4 comments

#37 - Warning with deprecrated feature in ggplot

Issue - State: closed - Opened by Bizes 9 months ago - 2 comments

#36 - error in normalization

Issue - State: closed - Opened by fionamassspec 12 months ago - 1 comment

#35 - Is log2-transformed the output data?

Issue - State: closed - Opened by froz9 about 1 year ago - 3 comments

#34 - Clean up NormalyzerDE dependencies

Issue - State: closed - Opened by Jakob37 about 1 year ago

#33 - Fixing crash and deprecation issues

Pull Request - State: closed - Opened by Jakob37 about 1 year ago - 3 comments

#32 - Error in analyzeNormalizations

Issue - State: closed - Opened by jangrasicOIST over 1 year ago - 12 comments
Labels: bug, breaking

#31 - analyzeNormalizations, the categoricalAnova parameter not used

Issue - State: closed - Opened by IgnatiusPang over 1 year ago - 2 comments
Labels: bug

#30 - Why plotting first sample in MA plot and first two samples in Scatter Plots

Issue - State: closed - Opened by lisiarend almost 2 years ago - 2 comments

#29 - Output .txt datasets gene names formatted to dates

Issue - State: closed - Opened by L3ft2di3 about 2 years ago - 2 comments

#28 - Error in prcomp.default(t(dataDf[stats::complete.cases(dataDf), ])

Issue - State: closed - Opened by ofleitas about 2 years ago - 8 comments

#27 - Crash in ANOVA calculations due to too few valid values crashes NormalyzerDE

Issue - State: closed - Opened by Jakob37 over 2 years ago
Labels: bug

#26 - NormalyzerDE crashes when missing data is present in "RT" column

Issue - State: closed - Opened by Jakob37 almost 3 years ago
Labels: bug

#25 - How to perform local normalization?

Issue - State: closed - Opened by Jeff-Gui almost 3 years ago - 3 comments

#24 - Include design matrix in output when running locally

Issue - State: closed - Opened by Jakob37 almost 4 years ago
Labels: enhancement

#23 - Running with Limited Numbers of Features

Issue - State: closed - Opened by delucalab almost 4 years ago - 3 comments

#22 - Sample names starting with numbers not understood

Issue - State: closed - Opened by Jakob37 over 4 years ago
Labels: bug

#21 - Clarification of file paths in vignette

Issue - State: closed - Opened by Jakob37 over 4 years ago
Labels: minor

#20 - Include the design matrix in the results folder

Issue - State: closed - Opened by Jakob37 over 4 years ago
Labels: enhancement

#19 - More flexible differential expression for incorporation in workflows

Issue - State: closed - Opened by Jakob37 over 4 years ago
Labels: enhancement

#18 - PDF reports for normalization can be very slow to load

Issue - State: closed - Opened by Jakob37 over 4 years ago - 1 comment
Labels: enhancement

#17 - Unclear errors for sparse dataset with many groups

Issue - State: closed - Opened by Jakob37 over 4 years ago
Labels: enhancement

#16 - Display of group numbers in report

Issue - State: closed - Opened by Jakob37 almost 5 years ago - 1 comment

#15 - rows with less that one non-NA in a group

Issue - State: closed - Opened by Luq16 almost 5 years ago - 2 comments
Labels: enhancement

#14 - Slow plotting functions

Issue - State: closed - Opened by Jakob37 almost 5 years ago
Labels: enhancement

#13 - Trouble with "noLogTransform" for large numbers

Issue - State: closed - Opened by Jakob37 almost 5 years ago - 1 comment

#12 - Allow spaces in sample names for normalization

Issue - State: closed - Opened by Jakob37 about 5 years ago - 2 comments
Labels: bug, minor

#11 - Non-numeric group level crashes contrasts

Issue - State: closed - Opened by Jakob37 about 5 years ago - 2 comments
Labels: bug

#10 - Calculate DE stats for rows with NA values

Issue - State: closed - Opened by flevander about 5 years ago - 1 comment
Labels: enhancement

#9 - Input verification of MaxQuant input data fails

Issue - State: closed - Opened by flevander over 5 years ago - 1 comment

#8 - Values of 0.0 throw an error

Issue - State: closed - Opened by arnscott almost 6 years ago - 7 comments

#7 - Switch tsv to txt file ending in output

Issue - State: closed - Opened by Jakob37 almost 6 years ago - 1 comment
Labels: enhancement

#6 - Error converting 0's to NAs

Issue - State: closed - Opened by arnscott about 6 years ago - 1 comment

#5 - Sample names with spaces doesn't work in DE part

Issue - State: closed - Opened by Jakob37 about 6 years ago - 2 comments
Labels: bug, minor

#4 - Output PDF get very large

Issue - State: closed - Opened by Jakob37 about 6 years ago - 1 comment
Labels: enhancement

#3 - Allow log2-transformed values as input to normalization module

Issue - State: closed - Opened by Jakob37 over 6 years ago - 1 comment
Labels: enhancement

#2 - Prevent graphical window popup when performing local processing

Issue - State: closed - Opened by Jakob37 over 6 years ago
Labels: minor

#1 - Input checking in normalyzerDE command

Issue - State: closed - Opened by Jakob37 over 6 years ago - 1 comment
Labels: bug, minor

GitHub / ComputationalProteomics/NormalyzerDE issues and pull requests