aertslab SCENIC issues - Githubissues

aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.

http://scenic.aertslab.org

GNU General Public License v3.0

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issues

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Can this be used for bulk-tissue data?

#467 guandailu opened 2 months ago
0
Error in runGenie

#464 arao0912 closed 2 months ago
0
initializeScenic(org="hgnc", dbDir="cisTarget_databases", nCores=1)

#461 YSYL-FSH opened 4 months ago
0
Bioconductor version

#459 flde closed 4 months ago
2
shiny::runApp NOT FOUND

#455 TZUwang opened 6 months ago
1
No questions here, please! runSCENIC_3_scoreCells :Error in signif(trhAssignment, 3)

#454 ManarHashemTaha opened 6 months ago
0
Error in file(con, "w") : all connections are in use

#453 TZUwang opened 6 months ago
2
Installation Error

#451 parkjooyoung99 opened 8 months ago
1
Running GRNBoost as a batch job

#449 MehvesOzel opened 8 months ago
0
could not find function "AUCell_createViewerApp"

#448 Eunice0519 opened 8 months ago
2
what is the difference between "motifAnnotations" and "motifAnnotations_hgnc_v9" , and what impact will it have on the results?

#447 Chenchen3Chen opened 8 months ago
0
Could not initialize SCENIC

#446 synatkeamsk opened 8 months ago
1
Scenic on HPC

#445 Sogand65 opened 9 months ago
1
Details about plot SCENIC results with cytoscape

#443 DiracZhu1998 opened 9 months ago
1
Mis-labelled motifs - SCENIC+

#442 JaanaB1 closed 9 months ago
1
Error Running runGenie3 in R

#441 DomenicoSkyWalker89 closed 9 months ago
3
Error message during running runSCENIC_3_scoreCells()

#439 jiuquzjw opened 10 months ago
6
run_SCENIC_2_createRegulons(): Warning

#438 btsanketh opened 10 months ago
1
RSS top eRegulon jaccard heatmap

#436 alirosen opened 10 months ago
0
Error in running runSCENIC_3_scoreCells() and AUCell_buildRankings() functions.

#434 DiracZhu1998 closed 10 months ago
3
addresses issue 168 by parameterizing checkAnnots rnktype

#432 blaserlab opened 11 months ago
0
error in plot_eRegulon function for downstream analysis

#431 alirosen closed 10 months ago
0
Warning in .AUCell_calcAUC(geneSets = geneSets, rankings = rankings, nCores = nCores,

#429 rraky opened 11 months ago
0
scenicOptions <- runSCENIC_2_createRegulons(scenicOptions, coexMethod=c("top5perTarget")) #** Only for toy run!!

#428 kakaisi opened 11 months ago
0
runSCENIC_3_scoreCells error

#427 alisyedraza1 opened 1 year ago
2
runSCENIC_3_scoreCells() error

#425 alisyedraza1 opened 1 year ago
3
TF dropout when running runSCENIC_2_createRegulons(scenicOptions)

#424 rmauron opened 1 year ago
0
No questions here, please!

#423 alisyedraza1 opened 1 year ago
1
Comparison between two SCENIC networks

#419 miguecass opened 1 year ago
1
exportsForArboreto input matrix log transformed or not

#418 iichelhadi opened 1 year ago
0
These errors seem to be related to the R version...

#416 jwg054000 opened 1 year ago
0
p-value of regulon activity calculation

#409 wingkyBs opened 1 year ago
0
Error in matrix(data = 0L, nrow = mat@Dim[1], ncol = mat@Dim[2])

#404 amini-sahand opened 1 year ago
0
Installation issue because of 'arrow' package

#401 abspangler13 opened 1 year ago
0
Error in runSCENIC_3_scoreCells

#400 AritaZ-hang opened 1 year ago
3
The clustering was not obvious.

#399 CHNLMENG opened 1 year ago
0
RcisTarget question

#397 zhangjiahao1234 opened 1 year ago
1
Installation error

#396 Jokendo-collab opened 1 year ago
0
✖ Column `features` doesn't exist.

#394 beetlejuice007 opened 1 year ago
2
runSCENIC_3_scoreCells errors: Not enough regulons with at least 10 genes.

#392 sanderslhc opened 1 year ago
0
Error in setting scenicOptions, what should I do?

#391 liuhy86 opened 1 year ago
0
Error in match.arg(method) : 'arg' must be of length 1 when running runSCENIC_2_createRegulons

#389 trucnguyen89 closed 1 year ago
0
pySCENIC cannot reproduce AUCell + tSNE projection from a tutorial

#388 ninhleba opened 1 year ago
1
Error in asMethod(object) : Cholmod error 'problem too large' at file ../Core/cholmod_dense.c, line 102 Calls: as.matrix -> as.matrix.Matrix -> as -> asMethod

#385 ekinsnmz opened 1 year ago
0
reduce number of top regulons per cell type

#383 azwainCC opened 1 year ago
0
Please reopen "Problem with initializeScenic() #168"

#379 huhayahoo opened 1 year ago
2
could not find function "calcRSS"

#374 chenx9 opened 1 year ago
7
How to apply SCENIC to zebrafish except for human,mouse and fly at the initializeScenic step?

#371 rlawltn9718 opened 1 year ago
1
AUC scores calulation

#368 xiebb7 opened 1 year ago
0
hg19-500bp-upstream-7species.mc9nr.feather file is missing in cisTarget database

#367 zhouxw27 closed 1 year ago
0