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lmweber
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diffcyt
R package for differential discovery analyses in high-dimensional cytometry data
MIT License
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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
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