Ecosyste.ms: Issues

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GitHub / lmweber/diffcyt issues and pull requests

#58 - Insights into data transformation

Issue - State: open - Opened by Thapeachydude 2 months ago - 2 comments

#57 - Comparison to Wilcox

Issue - State: closed - Opened by EST09 7 months ago - 5 comments

#56 - Please add the option to use clustering in colData

Issue - State: open - Opened by purisuto 10 months ago - 2 comments

#54 - How does diffcyt calculate logFC?

Issue - State: open - Opened by LukaTandaric 11 months ago

#53 - Possible bugfix for LMM fit outputting NAs for all comparisons

Issue - State: open - Opened by lmweber about 1 year ago - 2 comments

#52 - calcCounts is Set Up Incorrectly

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

#51 - diffCyt and edgeR return different results

Issue - State: open - Opened by LazDaria about 1 year ago

#49 - Diffcyt for two different columns

Issue - State: open - Opened by shanh1 over 1 year ago - 1 comment

#48 - Sorting x-axis in Heatmap

Issue - State: open - Opened by Almr95 over 1 year ago

#47 - createContrast help

Issue - State: closed - Opened by shanh1 over 1 year ago - 1 comment

#46 - Association with subject-level continuous phenotypes

Issue - State: open - Opened by hruffieux almost 2 years ago

#44 - Is clustering consistent over comparison of multiple levels?

Issue - State: closed - Opened by cr2106 about 2 years ago

#42 - Integration w/ FCS Express

Issue - State: closed - Opened by tdfy over 2 years ago - 1 comment

#41 - design & constrast matrix

Issue - State: open - Opened by cr2106 over 2 years ago - 4 comments

#40 - Check for state markers before diffcyt() DS test

Pull Request - State: open - Opened by igordot over 2 years ago

#38 - diffcyt-DA-edgeR Design and Contrast

Issue - State: closed - Opened by crchinfatt over 2 years ago - 1 comment

#37 - DA for multiple treatments

Issue - State: open - Opened by MayaCyTOFnewbie over 2 years ago - 3 comments

#36 - issue with setting up design/contrast matrices for DA/DS testing with catalyst SCE

Issue - State: closed - Opened by jenkinmt about 3 years ago - 2 comments

#35 - error with wrapper diffcyt() function

Issue - State: closed - Opened by jenkinmt about 3 years ago - 2 comments

#34 - very early error reading .fcs files in

Issue - State: closed - Opened by jenkinmt about 3 years ago - 4 comments

#33 - Manual gating input for DA clusters

Issue - State: closed - Opened by EAC-T about 3 years ago - 1 comment

#32 - NA's after DA-GLMM

Issue - State: open - Opened by yghosheh over 3 years ago - 1 comment

#30 - createContrast output for comparing multiple levels

Issue - State: open - Opened by MartijnVNL over 3 years ago

#29 - Input for createContrast()

Issue - State: open - Opened by JudithBernett over 3 years ago - 2 comments

#28 - #N/A in expression markers values

Issue - State: open - Opened by algebio over 3 years ago - 1 comment

#27 - diffcyt for longitudinal data

Issue - State: open - Opened by antoine4ucsd almost 4 years ago

#26 - Issue running DA analysis

Issue - State: open - Opened by carl-coyle almost 4 years ago - 1 comment

#25 - Model is nearly unidentifiable: very large eigenvalue

Issue - State: open - Opened by algebio almost 4 years ago - 5 comments

#24 - Censored predictors in differential abundance analysis

Pull Request - State: closed - Opened by retogerber almost 4 years ago - 1 comment

#22 - topTable function: show_logFC argument doesn't work

Issue - State: open - Opened by jdhogan about 4 years ago - 3 comments

#21 - Error plotting heatmap

Issue - State: open - Opened by tammyyyx about 4 years ago - 3 comments

#20 - markers_to_test = what?

Issue - State: open - Opened by amerji93 about 4 years ago - 5 comments

#19 - Error when comparing merged clusters

Issue - State: closed - Opened by poconnel3 about 4 years ago - 6 comments

#18 - Diffcyt on SCE - Error in glmFit.default()

Issue - State: open - Opened by sudu87 over 4 years ago

#17 - Mixed Model and Contrast

Issue - State: open - Opened by vivek-verma202 over 4 years ago - 1 comment

#16 - Compare only 2 out of many levels

Issue - State: open - Opened by LenaMayer over 4 years ago - 35 comments

#15 - CONTRAST DOUBT

Issue - State: closed - Opened by DomenicoSkyWalker89 over 4 years ago - 2 comments

#14 - Error running differential analysis on diffcyt

Issue - State: closed - Opened by FedericaOrsenigo over 4 years ago - 3 comments

#13 - error on diffcyt

Issue - State: closed - Opened by joe-jhou2 over 4 years ago - 1 comment

#12 - diffcyt() contrasts , when comparing two out of 4 conditions in the data

Issue - State: closed - Opened by paulyashna over 4 years ago - 1 comment

#11 - CATALYST older versions

Issue - State: closed - Opened by paulyashna over 4 years ago

#10 - plotHeatmap function

Issue - State: closed - Opened by Terskikh over 4 years ago - 2 comments

#9 - differential state analysis fails

Issue - State: closed - Opened by ramay over 4 years ago - 4 comments

#8 - extracting medians

Issue - State: closed - Opened by 83years over 4 years ago - 1 comment

#7 - customized weight in testDS_LMM

Issue - State: closed - Opened by fionarhuang about 5 years ago - 1 comment

#6 - Fix weight

Pull Request - State: closed - Opened by fionarhuang about 5 years ago

#5 - testDA_edgeR returns NA for some clusters

Issue - State: closed - Opened by ramay over 5 years ago - 6 comments

#4 - make all message() calls conform to verbose

Pull Request - State: closed - Opened by markrobinsonuzh over 5 years ago - 2 comments

#3 - Build failure on BioC-devel due to Vignette/ExperimentHub

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

#2 - add 'metadata' slot to keep track of clustering used for differential…

Pull Request - State: closed - Opened by HelenaLC almost 6 years ago - 1 comment

#1 - Automatically add group IDs to rowData of 'd_se'

Issue - State: closed - Opened by lmweber about 7 years ago - 1 comment