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aertslab
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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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Motif Database Error When Running Example Code
#361
pagarwal14
opened
1 year ago
1
Error at runSCENIC_3_scoreCells step
#359
maxc2020
opened
1 year ago
1
initializeScenic: getDbAnnotations error
#356
hernandezvargash
opened
1 year ago
7
initializeScenic
#350
ekinsnmz
opened
1 year ago
3
Parallelization of runCorrelation
#337
BenjaminDEMAILLE
opened
1 year ago
2
Error in `.rowNamesDF<-`(x, value = value) : invalid 'row.names' length
#335
ishwarvh
opened
1 year ago
1
feather v1 or v2 for R package
#334
zji90
opened
1 year ago
15
Error in gzfile(file, mode) : cannot open the connection
#333
caoligang-git
opened
1 year ago
1
hg19-500bp-upstream-7species.mc9nr.feather file is not available for download
#332
ZainulArifin1
closed
1 year ago
2
Number of regulons per cell type modification?
#326
IlianCx
opened
1 year ago
0
Error in AUCell step
#324
wbf520qcp
opened
1 year ago
1
Error: Cannot find cell information named 'CellType (it should be a column of the 'cellInfo')
#323
SidG13
opened
1 year ago
0
Average regulon activity by cluster
#322
GreyRockIQ
opened
1 year ago
0
build_loom error
#321
GreyRockIQ
closed
1 year ago
0
Question about cisTarget_databases
#320
YMSWhuang
opened
1 year ago
3
Error in hg19-500bp-upstream-10species.mc9nr.feather
#315
daeun301
opened
1 year ago
1
Error in scenicOptions
#311
ahsr-cell
closed
2 years ago
1
not able to install on hpc cluster
#310
wbf520qcp
opened
2 years ago
3
runSCENIC_2_createRegulons(scenicOptions) cannot proceed after scoring database (don't know if it is really running)
#307
parkjooyoung99
opened
2 years ago
2
Warning in .AUCell_calcAUC: Using only the first 14 genes (aucMaxRank) to calculate the AUC.
#302
zhang-TD
closed
2 years ago
1
Error in h(simpleError(msg, call))
#300
mrStrunge
closed
2 years ago
0
R crashes on SCENIC Initialization
#297
alejoaa
opened
2 years ago
2
Error : runSCENIC_3_scoreCells
#293
lagom2728
opened
2 years ago
3
Error in runSCENIC_2_createRegulons: object 'indexCol' not found
#290
monnneee
closed
1 week ago
15
Visualize and Finalize the Result
#279
HocheolJang426
closed
2 years ago
0
R crashes on SCENIC Initialization
#238
NickNolan
closed
2 years ago
4
runSCENIC_3_scoreCells error: columns not found
#237
shexiaolu
opened
2 years ago
2
Questions?
#236
s-aibar
closed
2 years ago
1
Help with manual inspection of AUCell histogram for regulon binerization
#235
Jeron1996
closed
2 years ago
0
Cannot use Integrated data in SCENIC
#234
Lumskie
closed
2 years ago
1
identify regulons - custom gene list
#233
paolo-kunderfranco
closed
2 years ago
0
Finding TF activity for each cluster in TSNE
#232
Lumskie
closed
2 years ago
0
Why could a motif be enriched at 500bpUS and 100bpDS of TSS but not at 10kbp centered?
#231
charlesgwellem
closed
2 years ago
0
Loosing too many genes
#230
charlesgwellem
closed
2 years ago
0
Extracting regulon activity matrix
#229
Lumskie
closed
2 years ago
0
unable to find an inherited method for function ‘GENIE3’ for signature ‘"dgeMatrix"’
#228
ML1990-Lab
closed
2 years ago
2
runSCENIC_3_scoreCells (Error in readRDS)
#227
wwh199459
opened
2 years ago
1
"ERROR 403: Forbidden." when downloading RcisTarget databases from resources.aertslab.org
#226
hffqyd
closed
2 years ago
2
Do you have any suggestions about SCENIC for other species other species ?
#225
gloriafight
closed
2 years ago
1
parallelization problem in R?
#224
MilanPicard
closed
2 years ago
0
Error: failed to stop 'SOCKcluster* cluster: ignoring SIGPIPE signal
#223
db381x
closed
2 years ago
1
R is aborted when running initializeScenic
#222
lucyu2668
opened
2 years ago
3
The outputs are instable
#221
XinWang19
closed
2 years ago
1
How can we access Cell ID, tSNE Coordinates and Clustering metadata from SCENIC?
#218
AAA-3
closed
2 years ago
1
Error in runSCENIC_2_createRegulons()
#217
ZJ-zuojing
opened
2 years ago
4
SCENIC on demultiplexing cell hashing results
#216
fouerghi
closed
2 years ago
0
importModulesGmt doubt
#215
rosanababu
closed
2 years ago
0
Difference results between R SCENIC and pySCENIC
#213
ayumatsubo
closed
2 years ago
0
runSCENIC_4_aucell_binarize ERROR
#211
ryrl970311
opened
2 years ago
2
ERROR in runSCENIC_2_createRegulons
#210
ryrl970311
opened
2 years ago
2
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