hemberg-lab SC3 issues - Githubissues

hemberg-lab / SC3

A tool for the unsupervised clustering of cells from single cell RNA-Seq experiments

http://bioconductor.org/packages/SC3

GNU General Public License v3.0

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issues

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Question about <NA> labels from cell clustering via SC3

#111 yxy92 closed 5 months ago
1
sc3_run_svm has a prediction issue

#110 jmuribes closed 1 year ago
2
Running SC3 in integrated data

#109 anemartinezlarrinaga2898 closed 1 year ago
1
could not find function "calculate_distance"

#108 irtisha opened 1 year ago
2
long vectors are not supported in .C

#107 zhangtongda closed 2 years ago
1
Saving SC3 clustering output as csv files

#106 bsamal20 closed 2 years ago
3
saving SC3 output

#105 bsamal20 opened 2 years ago
0
rewritten parallelism to BiocParallel package

#104 gorgitko opened 3 years ago
6
one node produced an error: Error in ED2(data)

#103 eshraaqsaeed opened 3 years ago
1
The Perl script 'WriteXLS.pl' failed to run successfully.

#102 UnkownNames opened 3 years ago
0
Error in rowSums(out_pathway) : 'x' must be an array of at least two dimensions

#101 zina-R closed 3 years ago
1
sc3_kmeans produces "Warning message: Quick-TRANSfer stage steps exceeded maximum (= 250000)"

#100 MikeHala closed 3 years ago
1
Which remove-batch-effect package work best with SC3?

#99 kuang-da closed 4 years ago
1
Sparse matrix causes errors

#98 RebekkaWegmann closed 4 years ago
2
Error in prcomp.default

#97 dsimps1993 closed 4 years ago
4
each element of 'reducedDims' must be a matrix-like object with nrow equal to 'ncol(object)

#96 makimenkova opened 4 years ago
1
Gene names lost after get_marker_genes()

#95 friedue opened 5 years ago
0
Plot expression on given list of genes

#94 shabs24 closed 5 years ago
1
Clustering for more than 10000 Genes

#93 hkarakurt8742 closed 5 years ago
3
SC3 with Batch Correction

#92 hkarakurt8742 closed 5 years ago
1
How to calculate D?

#91 XiHuYan closed 5 years ago
4
Copy transformations to @reducedDims when possible

#90 nh3 closed 5 years ago
0
Fixed the sparse matrix issue

#89 zhangguy opened 5 years ago
1
error running sc3_plot_de_genes

#88 qiaowei-vvjoe opened 5 years ago
8
No gene names in export results

#87 dsimps1993 opened 5 years ago
4
SC3 error on linux server: Not compatible with requested type

#86 LuyiTian closed 5 years ago
5
Which data type for clustering

#85 mkrzak closed 5 years ago
2
sc3_plot_de_genes and sc3_plot_markers problems

#84 Santos22903 closed 5 years ago
2
Consider using Forks for parallelism?

#83 Shians closed 3 years ago
3
is it possible to surpress the message in `sc3` function.

#82 LuyiTian opened 5 years ago
1
#UMI counts table

#81 penglbio closed 5 years ago
1
Small suggestion for sc3_prepare() documentation

#80 PeteHaitch opened 5 years ago
1
Plot column names

#79 simone-rizzetto opened 5 years ago
1
Specify custom genes/features

#78 royfrancis closed 5 years ago
1
Clusters for max 5000 cells

#77 julien-roux closed 5 years ago
2
SC3 repeatedly loads packages while running and has data display issues

#76 jamesrhowe closed 5 years ago
3
Not clear how SC3 exactly works

#75 CodeInTheSkies closed 5 years ago
5
Error in checkForRemoteErrors(val) : 3 nodes produced errors; first error: Error in ED2(data) : Not compatible with requested type: [type=S4; target=double].

#74 JesusCorria closed 5 years ago
2
Error in `[.default`(clusts, , paste0("sc3_", hash.table[i, 1], "_clusters"))

#73 DrLucyMac opened 5 years ago
10
Error in checkForRemoteErrors(val) :

#72 15084921898 closed 5 years ago
2
Excluding principal components from clustering

#71 martabrozynska closed 5 years ago
2
Annotation colour palette in heatmaps

#70 wikiselev opened 6 years ago
0
Pass k_estimate results if ks is NULL; fixes #67

#69 pati-ni closed 6 years ago
0
Large number of NA's when run on large dataset.

#68 TChan92 closed 5 years ago
17
k_estimator output not passed to sc3 wrapper function

#67 leonfodoulian closed 6 years ago
1
Feature request: option to specify assay used

#66 dkoppstein closed 5 years ago
5
show_pdata errors in sc3_plot_expression(), sc3_plot_de_genes(), sc3_plot_markers(), but not sc3_plot_consensus()

#65 KeelyDulmage closed 5 years ago
4
Error in ED2(data)

#64 biosyssun closed 5 years ago
3
default for `n_cores`

#63 stephaniehicks closed 6 years ago
1
export plot from SC3

#62 MichaelPeibo closed 6 years ago
2