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cole-trapnell-lab
/
cicero-release
https://cole-trapnell-lab.github.io/cicero-release/
MIT License
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Adding fData
#52
sel041
closed
4 years ago
0
multi-sample
#51
TheSallyGardens
closed
4 years ago
1
argument "maxbp" is missing, with no default
#50
ccruizm
closed
4 years ago
0
Issues with Cicero gene activity score
#49
mitian223
closed
4 years ago
2
Could not find function "newCellDataSet"
#48
cartal
closed
4 years ago
2
Question for aggregated cells
#47
hejing3283
closed
4 years ago
2
Question for trajector analysis
#46
crushseven-7
closed
4 years ago
2
how to compare two sample using plot_connections
#45
honghh2018
closed
4 years ago
1
plot_accessibility_in_pseudotime update to work with Monocle 3
#44
domcke
closed
1 year ago
6
How to use gene activity matrix in plot_cells & mm10 genome to view connections?
#43
sta1245work
closed
4 years ago
1
Error in `[.data.table`(bedpedata, , i)
#42
danhtruong
closed
4 years ago
3
estimateDispersion Issue
#41
zillerm
closed
4 years ago
2
plot_connections issued error for specific range position
#40
honghh2018
closed
4 years ago
6
Plot_connections: Error in `$<-.data.frame`(`*tmp*`, "feature", value = character(0)) : replacement has 0 rows, data has 101
#39
yzh2017
closed
4 years ago
1
About CellDataSet and cell_data_set
#38
dhoneyi
closed
4 years ago
1
Deal with no 'chr' in plot_connections
#37
hpliner
closed
4 years ago
2
Deal with plot_connections NAs
#36
hpliner
closed
4 years ago
0
Questions regarding to "plot_connections", "plot_cells" and "new_cell_data_set", thank you for your help.
#35
MQMQ2018
closed
4 years ago
7
It looks like a conflint between monocle::detectGenes and new_cell_data_set function in Cicero for monocle3? Could you help to give me some tips to figure it out? Thank you so much.
#34
MQMQ2018
closed
5 years ago
2
Is there "data(gene_annotation_sample)" file for hg38 in cicero in step of Constructing cis-regulatory networks? Thank you so much.
#33
MQMQ2018
closed
5 years ago
2
Running cicero on bulk data
#32
amr15
closed
5 years ago
1
Link to a page is broken.
#31
sameet
closed
5 years ago
6
Compatibility with Monocle3
#30
jeremycfd
closed
5 years ago
5
Handling large dataset
#29
marianogabitto
closed
5 years ago
2
Errors in plot_connections
#28
Austin-s-h
closed
5 years ago
0
Transfer to travis.com
#27
hpliner
closed
1 year ago
0
Make promoter annotation clearer in gene activity section
#26
hpliner
closed
5 years ago
0
Error in preprocessing
#25
smanne07
closed
5 years ago
9
Error in reduce dimension part of trajectory analysis
#24
smanne07
closed
5 years ago
2
scale of the normalized the gene activity matrix
#23
crazyhottommy
closed
5 years ago
6
ERROR:duplicate 'row.names' are not allowed
#22
yxaxaxa
closed
5 years ago
2
annotation of genes needs to take strandness into account?
#21
crazyhottommy
closed
5 years ago
4
last step for normalizing the gene activity scores failed
#20
crazyhottommy
closed
5 years ago
12
How to prepare input data for atac-seq trajectory as "cicero_data"?
#19
x811zou
closed
5 years ago
5
Add a check for chr_UN/chr_random in make_input_cds
#18
hpliner
closed
4 years ago
0
Monocle 3 alpha compatibility issue
#17
hpliner
closed
5 years ago
0
Speed improvement in make_cicero_cds function.
#16
shamoni
closed
5 years ago
2
Add FAQ
#15
hpliner
closed
5 years ago
0
Add check for zero rows in normalize gene activities
#14
hpliner
closed
5 years ago
1
Add documentation support for 10x scATAC output
#13
hpliner
closed
5 years ago
0
using non-UCSC chromosome name formats in plot_connections()
#12
tdurham86
closed
4 years ago
1
Fix docs style issues, consolidate and remove files
#11
jdomingu
closed
5 years ago
1
Release 3 8
#10
hpliner
closed
5 years ago
0
Question about differentialGeneTest
#9
danielee0707
closed
5 years ago
1
Filtering genomic_coords in estimate_distance_parameters() ?
#8
hypercompetent
closed
5 years ago
2
Error with creating cicero CDS
#7
eliduong
closed
5 years ago
10
Updates to make_cicero_cds() to increase speed.
#6
hypercompetent
closed
5 years ago
0
Aggregating Co-Accessible Peaks
#5
yanwu2014
closed
6 years ago
1
Benchmarks
#4
jgranja24
closed
6 years ago
0
make_atac_cds: fData(atac_cds)$chr <- as.numeric(as.character(fData(atac_cds)$chr))
#3
cbravo93
closed
6 years ago
1
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