csbl-usp CEMiTool issues

csbl-usp / CEMiTool

Co-Expression Module Identification Tool (CEMiTool) official repository

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issues

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Interaction networck: Unlabeled data points (too many overlaps)

#101 Henrique-reolon closed 4 months ago
2
The `fun.y` argument of `stat_summary()` is deprecated as of ggplot2 3.3.0.

#100 Henrique-reolon closed 6 months ago
2
Getting unused argument error through Docker with sample data and own data

#99 kashishky opened 9 months ago
0
Problems formating GMT file

#98 Mxrcon closed 11 months ago
3
CEMiTool on proteomics abundance

#97 raulfalcao closed 1 year ago
1
Big module is not enriched in GSEA

#96 mohamadysn opened 1 year ago
0
Difference between the results obtained with Rscript and the results obtained from the Cemitool site

#95 mohamadysn closed 1 year ago
1
Installation error

#94 scottgigante-immunai closed 2 years ago
1
Error in .local(cem, ...) : Sample annotation file does not contain all samples in expression file. Please input new sample annotation file using function sample_annotation()

#93 jacraft closed 2 years ago
6
Clarification for network_type argument

#92 ruchiups closed 2 years ago
1
Difference between profile plot and GSEA

#91 pedrostrusso closed 2 years ago
3
Hub genes in interaction plots displaying with low connectivity?

#90 NickFiore-1 closed 2 years ago
8
Missing interaction network for module

#89 NickFiore-1 closed 2 years ago
8
How to calculate logFC and p-value of co-expressed modules across different samples?

#88 kaanokay closed 2 years ago
4
Output of hierarchical clustered modules and eigengene plots

#87 brettChapman closed 2 years ago
1
Beta value not found

#86 brettChapman closed 2 years ago
1
Interpreting gsea plot

#85 hansong798 closed 2 years ago
1
Deciphering PPI network

#84 kphelan13 closed 2 years ago
3
Os primeiros três módulos não são lotados na aba ORA representation

#83 victortoledo closed 3 years ago
1
Error while running through singularity container

#82 brettChapman closed 3 years ago
10
how to obtain the mouse protein-protein interaction file？

#81 thekingofall closed 3 years ago
1
cemitool() fails if input is tibble

#80 BaxW closed 3 years ago
1
Annotating neighboring genes in hub gene networks

#79 phoebe460 closed 3 years ago
1
Trouble interpreting differences in hub genes from interaction networks.

#78 kylepalos closed 3 years ago
2
NA values to some modules

#77 lukais-i0han closed 3 years ago
4
Question on files in extdata

#76 ruchiups closed 3 years ago
2
Clarification request on module significance in GSEA,ORA

#75 ruchiups closed 3 years ago
5
Issue with specifying parameter beta

#74 ashaypatel closed 3 years ago
3
nmodules(cem) says I have 3 modules but I only see 2 plotted on the GSEA heatmap

#73 ashaypatel closed 3 years ago
2
Errors when expression matrix has NAs

#72 allakarpova closed 3 years ago
3
how to infer the hub gene ?

#71 cqneosun closed 3 years ago
6
Issues when calling diagnostic_report from within another markdown

#70 komalsrathi closed 3 years ago
4
Changing Colors When Plotting Interaction Networks for Multiple Modules

#69 phoebe460 closed 3 years ago
1
how to get the interaction gene id in label in the interaction network?

#68 cqneosun closed 3 years ago
1
what does the file selected genes.txt mean?

#67 cqneosun closed 3 years ago
1
only disaply zero or less than ten hub genes in interaction work

#66 cqneosun closed 3 years ago
0
ORA and PPI networks Clarification

#65 phoebe460 closed 3 years ago
2
why some module with empty GSEA NES and p value?

#64 cqneosun closed 3 years ago
4
troube in cemitool

#63 cqneosun closed 3 years ago
8
Running CEMiTool with multiple factors/conditions

#62 akcorut closed 3 years ago
2
Interpreting fGSEA plots

#61 phoebe460 closed 3 years ago
6
Could not specify the parameter Beta. No modules found.

#60 bjstewart1 closed 3 years ago
2
Cannot install in R/BiocManager, something about 'GO.db'?

#59 mr-september closed 3 years ago
1
identifying a cell's gene modules

#58 jasminelmah closed 3 years ago
4
CEMitools with negative PIC values

#57 jasminelmah closed 3 years ago
1
how to draw only 'interaction plot'

#56 a00101 closed 3 years ago
2
Generate_report not working

#55 gourivadali closed 3 years ago
13
No modules found

#54 gabrieljmarques closed 3 years ago
1
There were 6 pathways for which P-values were not calculated properly due to unbalanced gene-level statistic values

#53 saramasarone closed 4 years ago
2
subscripts out of bounds error

#52 kemguru2020 closed 2 years ago
1