Issues

diffcyt after CATALYST returned NA in diffcyt-DS-LMM even when clusters have "sufficient" number of cells across at least half of samples
lmweber/diffcyt#64 · opened on Mar 4, 2025
1
An update to edgeR
lmweber/diffcyt#63 · opened on Feb 10, 2025
2
ds analysis with multiple conditions
lmweber/diffcyt#60 · opened on Feb 1, 2025
1
T cell Subpopulation Percentage Showing as Zero in Differential Analysis Despite Presence in Clustering Results
lmweber/diffcyt#59 · opened on Aug 10, 2024
Insights into data transformation
lmweber/diffcyt#58 · opened on Jul 31, 2024
2
Please add the option to use clustering in colData
lmweber/diffcyt#56 · opened on Dec 19, 2023
2
Fixed the calcCounts and calcMedians Functions and Added Option to Choose Which Clustering Is Used
lmweber/diffcyt#55 · opened on Nov 3, 2023
1
How does diffcyt calculate logFC?
lmweber/diffcyt#54 · opened on Oct 24, 2023
Possible bugfix for LMM fit outputting NAs for all comparisons
lmweber/diffcyt#53 · opened on Sep 25, 2023
2
diffCyt and edgeR return different results
lmweber/diffcyt#51 · opened on Jul 21, 2023
Diffcyt for two different columns
lmweber/diffcyt#49 · opened on Jun 19, 2023
1
Sorting x-axis in Heatmap
lmweber/diffcyt#48 · opened on May 25, 2023
Association with subject-level continuous phenotypes
lmweber/diffcyt#46 · opened on Dec 13, 2022
Create design & contrast matrix for differential state analysis
lmweber/diffcyt#45 · opened on Sep 19, 2022
diffcyt differential expression model with patient_id as random effect only returns NA p values
lmweber/diffcyt#43 · opened on Jul 26, 2022
design & constrast matrix
lmweber/diffcyt#41 · opened on May 27, 2022
4
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
lmweber/diffcyt#39 · opened on May 23, 2022
DA for multiple treatments
lmweber/diffcyt#37 · opened on Feb 9, 2022
3
NA's after DA-GLMM
lmweber/diffcyt#32 · opened on Jun 11, 2021
1
low p values when using testDA_GLMM().. lme4 too sensitive to weights?
lmweber/diffcyt#31 · opened on Mar 9, 2021
1
createContrast output for comparing multiple levels
lmweber/diffcyt#30 · opened on Feb 1, 2021
Input for createContrast()
lmweber/diffcyt#29 · opened on Jan 18, 2021
2
#N/A in expression markers values
lmweber/diffcyt#28 · opened on Jan 4, 2021
1
diffcyt for longitudinal data
lmweber/diffcyt#27 · opened on Dec 25, 2020
3
Issue running DA analysis
lmweber/diffcyt#26 · opened on Nov 17, 2020
1