broadinstitute infercnv issues

broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq

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Successfully completed, but no plot...

#428 gdk43 opened 2 years ago
2
Where can I read an explanation of the InferCNV algorithm?

#427 nadavbra closed 2 years ago
1
Error Encountered during Step 15 "Error in paste(sig, collapse = "#") : (converted from warning) NAs introduced by coercion to integer range"

#426 bhabakd opened 2 years ago
16
does not work with new R 4.2.0

#425 morchalabi closed 2 years ago
2
infercnv results to compare to bulk WGS CNV

#424 kirakoko opened 2 years ago
3
More explicit error message when trying add_to_seurat without HMM

#423 matt-sd-watson closed 2 years ago
2
infercnv final object does not have cell name in the 'subcluster' slot

#422 andynkili closed 2 years ago
2
Error message when clustering samples (step15, version 1.12.0)

#421 chent5 closed 2 years ago
9
How to intepret box plot of cnvProbs.0.*.pdf?

#420 jsialar closed 2 years ago
2
CNVs removed after step 19 are still in the final plot (plots interpretation)

#419 andynkili closed 2 years ago
2
Error in rasterImage(as.raster(zc), min(x), min(y), max(x), max(y), interpolate = FALSE) :

#418 xiangrong7 closed 2 years ago
4
export to ngchm failed

#417 Sa753 closed 2 years ago
0
can issue #67 ('cell groups consisting of just one cell') be re-opened?

#416 plijnzaad opened 2 years ago
5
Error step 6

#415 Sa753 closed 2 years ago
3
Several times the results predicted by CNV cannot be repeated

#414 wanglx1998 closed 2 years ago
5
Code will not progress past step 8

#413 mnagy1716 closed 2 years ago
1
C stack usage XXX is too close to the limit (even after using "ulimit -s unlimited")

#412 angkoomin closed 2 years ago
1
how to load infercnv.observations_dendrogram.txt file in R

#411 Feng-Zhang closed 2 years ago
1
Error: match.arg(tumor_subcluster_partition_method)

#410 shalbahl closed 2 years ago
2
Tumour heterogeneity - visualising loss/gain in phylogenetic tree format

#409 angkoomin closed 2 years ago
2
Error in if (run_arguments$HMM) { : argument is of length zero

#408 gongmeiyuan closed 2 years ago
3
X11 problem

#407 tlz4320 closed 2 years ago
1
Error in .plot_cnv_references(ref_data = ref_data_t, ref_groups = ref_groups, : with R version 4.1.2 but same code working with R version 4.1.0 if I put cluster_by_groups=FALSE

#406 SaritaPoonia closed 2 years ago
1
Question about reload infercnv_obj

#405 Fish-on-plate closed 2 years ago
3
InferCNV for HMM cell mode

#404 cv55 closed 2 years ago
2
ModuleNotFoundError: No module named 'math'

#403 kirakoko closed 2 years ago
5
Infercnv failing on step 15;Error in hclust(dist(t(tumor_expr_data)), method = hclust_method) : N must be at least 2.

#402 ninashenker closed 2 years ago
5
InferCNV handling of small clusters

#401 wong-nw closed 2 years ago
3
Unexpected error when cluster_references=FALSE - missing parameter for plot_cnv() in postProbNormal()

#400 ChloeQuignot closed 2 years ago
2
STEP 13 problem detected with infercnv_obj

#399 andynkili closed 2 years ago
3
Infercnv "Error in rep(contig_name, contig_tbl[contig_name]) : invalid 'times' argument"

#398 plijnzaad closed 2 years ago
4
Extracting HMM features: Cell names in Seurat object and infercnv results do not match

#397 angkoomin closed 2 years ago
1
step 15 Error "NAs are not allowed in subscripted assignments"

#396 andynkili closed 2 years ago
4
Using average profile (across all cells) as a reference if reference normal cells are not provided

#395 RegnerM2015 closed 2 years ago
5
17_HMM_predHMMi6.hmm_mode-samples.pred_cnv_genes.dat file is empty

#394 raybueno closed 2 years ago
3
how to extract cnv score and plot it on UMAP

#393 xinmiaoyan closed 2 years ago
1
Data matrix with single-cell CNV calls

#392 elisafazz closed 2 years ago
1
Plot labels of malignant cells in a predefined order

#391 massonix closed 2 years ago
2
A question about reference cells

#390 inbarsh2 closed 2 years ago
5
Question about result interpretation

#389 TChen0730 closed 2 years ago
4
Cholmod error 'problem too large' at file

#388 talban14 closed 2 years ago
3
STEP 07: not enough cores available, setting to num avail cores: 1

#387 zhangjl-work closed 2 years ago
0
ngchm error about java

#386 Rui-Jing closed 2 years ago
2
Subclustering samples based on predefined groups

#385 angkoomin closed 2 years ago
1
FBI observation

#384 Sa753 closed 2 years ago
2
Is there a way to get the reference used for a sub cluster?

#383 tinakeshav closed 2 years ago
3
observation groups incomplete in heatmap

#382 andynkili closed 2 years ago
12
Error after installing version 1.11.1

#381 Sa753 closed 2 years ago
6
The proportion_scaled_cnv of all cells in observation group were identical??

#380 fengwei-li closed 2 years ago
1
Step 15 error: Error in unlist(object) : long vectors not supported yet:

#379 adhisadi closed 2 years ago
1

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