lmweber diffcyt issues - Githubissues

lmweber / diffcyt

R package for differential discovery analyses in high-dimensional cytometry data

MIT License

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issues

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T cell Subpopulation Percentage Showing as Zero in Differential Analysis Despite Presence in Clustering Results

#59 TongzhenXu opened 2 months ago
0
Insights into data transformation

#58 Thapeachydude opened 2 months ago
2
Comparison to Wilcox

#57 EST09 closed 7 months ago
5
Please add the option to use clustering in colData

#56 david-priest opened 10 months ago
2
Fixed the calcCounts and calcMedians Functions and Added Option to Choose Which Clustering Is Used

#55 LukaTandaric opened 12 months ago
1
How does diffcyt calculate logFC?

#54 LukaTandaric opened 1 year ago
0
Possible bugfix for LMM fit outputting NAs for all comparisons

#53 lmweber opened 1 year ago
2
calcCounts is Set Up Incorrectly

#52 LukaTandaric closed 12 months ago
0
diffCyt and edgeR return different results

#51 LazDaria opened 1 year ago
0
How to use diffcyt to identify differentially-expressed proteins/biomarkers of a cluster in flow cytometry data?

#50 denvercal1234GitHub closed 1 year ago
1
Diffcyt for two different columns

#49 shanh1 opened 1 year ago
1
Sorting x-axis in Heatmap

#48 Almr95 opened 1 year ago
0
createContrast help

#47 shanh1 closed 1 year ago
1
Association with subject-level continuous phenotypes

#46 hruffieux opened 1 year ago
0
Create design & contrast matrix for differential state analysis

#45 Stein-ErikG opened 2 years ago
0
Is clustering consistent over comparison of multiple levels?

#44 cr2106 closed 2 years ago
0
diffcyt differential expression model with patient_id as random effect only returns NA p values

#43 singlecellfan opened 2 years ago
0
Integration w/ FCS Express

#42 tdfy closed 2 years ago
1
design & constrast matrix

#41 cr2106 opened 2 years ago
4
Check for state markers before diffcyt() DS test

#40 igordot opened 2 years ago
0
Error in SummarizedExperiment: the rownames and colnames of the supplied assay(s) must be NULL or identical to those of the SummarizedExperiment object (or derivative) to construct

#39 igordot opened 2 years ago
0
diffcyt-DA-edgeR Design and Contrast

#38 crchinfatt closed 2 years ago
1
DA for multiple treatments

#37 MayaCyTOFnewbie opened 2 years ago
3
issue with setting up design/contrast matrices for DA/DS testing with catalyst SCE

#36 jenkinmt closed 3 years ago
2
error with wrapper diffcyt() function

#35 jenkinmt closed 3 years ago
2
very early error reading .fcs files in

#34 jenkinmt closed 3 years ago
4
Manual gating input for DA clusters

#33 EAC-T closed 3 years ago
1
NA's after DA-GLMM

#32 yghosheh opened 3 years ago
1
low p values when using testDA_GLMM().. lme4 too sensitive to weights?

#31 florian-bach opened 3 years ago
0
createContrast output for comparing multiple levels

#30 MartijnVNL opened 3 years ago
0
Input for createContrast()

#29 JudithBernett opened 3 years ago
2
#N/A in expression markers values

#28 algebio opened 3 years ago
1
diffcyt for longitudinal data

#27 antoine4ucsd opened 3 years ago
0
Issue running DA analysis

#26 carl-coyle opened 3 years ago
1
Model is nearly unidentifiable: very large eigenvalue

#25 algebio opened 3 years ago
5
Censored predictors in differential abundance analysis

#24 retogerber closed 3 years ago
1
Direction of comparison between the disease group and the reference group

#23 tammyyyx opened 4 years ago
0
topTable function: show_logFC argument doesn't work

#22 jdhogan opened 4 years ago
3
Error plotting heatmap

#21 tammyyyx opened 4 years ago
3
markers_to_test = what?

#20 amerji93 opened 4 years ago
5
Error when comparing merged clusters

#19 poconnel3 closed 4 years ago
6
Diffcyt on SCE - Error in glmFit.default()

#18 sudu87 opened 4 years ago
0
Mixed Model and Contrast

#17 vivek-verma202 opened 4 years ago
1
Compare only 2 out of many levels

#16 LenaMayer opened 4 years ago
35
CONTRAST DOUBT

#15 DomenicoSkyWalker89 closed 4 years ago
2
Error running differential analysis on diffcyt

#14 FedericaOrsenigo closed 4 years ago
3
error on diffcyt

#13 joe-jhou2 closed 4 years ago
1
diffcyt() contrasts , when comparing two out of 4 conditions in the data

#12 paulyashna closed 4 years ago
1
CATALYST older versions

#11 paulyashna closed 4 years ago
0
plotHeatmap function

#10 Terskikh closed 4 years ago
2