cole-trapnell-lab cicero-release issues

cole-trapnell-lab / cicero-release

https://cole-trapnell-lab.github.io/cicero-release/

MIT License

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issues

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Error: is(object = cds, class2 = "CellDataSet") is not TRUE

#103 GaF123 closed 1 month ago
1
error with run_cicero function

#102 lucyu2668 opened 4 months ago
1
Motif enrichment in the co-accessible sites

#101 momur closed 1 month ago
1
Problem installing cicero in CentOS 7.9

#100 massonix opened 6 months ago
1
practical suggestions to avoid an abrupt termination

#99 Puriney opened 7 months ago
1
I can't run the run_cicero!!!

#98 skkanlei opened 7 months ago
4
While running code "run_cicero", R studio server will terminate!!

#97 skkanlei opened 7 months ago
3
Update runCicero.R

#96 Puriney closed 1 month ago
0
Peak file for generating CDS

#95 rb56 closed 8 months ago
1
make_atac_cds() does not generate cell_data_set object

#94 ivykos closed 9 months ago
1
generate_ccans() Error: caught segfault: address 0x55e403466ee4, cause 'memory not mapped'

#93 ShihuiZhangsh opened 1 year ago
3
run_cicero Peak1 include NA

#92 zhangqc723 closed 1 month ago
3
Plot_connection axis label

#91 JunxiFeng closed 1 year ago
1
error about run_cicero

#90 vikon72 closed 1 month ago
4
Questions about make_cicero_cds function

#89 Abigail1l1l1l closed 1 year ago
1
Hi, question about start using cicero

#88 TauHHCC closed 1 year ago
2
length of Dimnames[[1]] (115668) is not equal to Dim[1] (147955)

#87 midichlorianrich closed 1 year ago
2
run_cicero error

#86 tkisss closed 1 year ago
2
no transcrition structures in plot_connection

#85 ccshao closed 1 year ago
1
every link duplicated in the results

#84 ccshao closed 2 years ago
1
reduceDimension:Error in if (any(i < 0L)) { : missing value where TRUE/FALSE needed

#83 yuxuanChen777 closed 1 year ago
3
interpretation of generate_ccans output

#82 pengxin2019 closed 2 years ago
1
[Cicero in GM12878/K562 cell lines data ]

#81 dhoneyi closed 2 years ago
1
Correlation between gene expression and cicero activity

#79 AnjaliC4 closed 2 years ago
1
Add ability to bin based on certain metadata

#78 hpliner opened 2 years ago
0
Is there any way to retrieve / assign aggregated cluster IDs to original cell labels?

#77 HaglundA closed 2 years ago
7
Error in (function (classes, fdef, mtable) : unable to find an inherited method for function 'exprs' for signature '"CellDataSet"'

#76 candacelei closed 2 years ago
2
How to extract dimension data after clustering in monocle3

#75 yanhaidong1 closed 3 years ago
2
plot_connects() font unreadable

#74 wfma closed 2 years ago
2
Handle the case when a peak overlaps with the promoter of two or more genes

#73 yushengak47 opened 3 years ago
1
Does cicero include negative correlations in co-accessibility?

#72 decapicone closed 3 years ago
4
quick ATAC-seq question

#71 widsquid closed 3 years ago
3
run_cicero multicore

#70 skilpinen opened 3 years ago
1
Transfering mapping info from one object to another

#69 aleksandrPi closed 3 years ago
4
Class compatibility issue between cicero3 (for monocle3) and monocle3.

#68 quinamatics closed 3 years ago
8
data("mouse.mm9.genome")

#67 elachtarajax closed 3 years ago
2
Error message when running aggregate_by_cell_bin()

#66 chent5 closed 4 years ago
2
Multiple peak tracks

#65 johannesnicolaus closed 4 years ago
2
Generating CCANs with inconsistent numbering

#64 genomaxx closed 4 years ago
1
Error installing Cicero

#63 sylestiel closed 4 years ago
2
Error message when running generate_ccans()

#62 chent5 closed 4 years ago
1
A question about generate_ccans() results

#61 chent5 closed 4 years ago
1
# cell ordering can be done interactively by leaving out "root_cells"

#60 sylestiel closed 4 years ago
1
Error fetching data from UCSC

#59 sylestiel closed 4 years ago
1
Error: is(object = cds, class2 = "CellDataSet") is not TRUE

#58 sylestiel closed 4 years ago
4
make_cicero_cds reports input object class error

#57 MagpiePKU closed 4 years ago
1
annotate_cds_by_site error with 10x genomics reference genome

#56 jindalk closed 4 years ago
3
run Cicero on whole data or subsets?

#55 Brawni closed 4 years ago
2
cannot go through reduceDimension()

#54 wangmhan closed 4 years ago
4
Enhancement - Matrix Multiplication in make_cicero_cds

#53 Austin-s-h opened 4 years ago
0