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hemberg-lab
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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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first error: Error in transf[, 1:hash.table$n_dim[i]] : incorrect number of dimensions
#61
Jayjay601
closed
6 years ago
15
Is there a way to pull out the stability index matrix from the SC3 object?
#60
yingzhang121
opened
6 years ago
7
Error in !isSpike(object) : invalid argument type
#59
yicheinchang
opened
6 years ago
3
Update calculate_stability.Rd
#58
tallulandrews
closed
6 years ago
1
Remove one N from the denominator of stability
#57
tallulandrews
closed
6 years ago
2
Performance Enhancements, Laplacian matrix improvements
#56
pati-ni
closed
6 years ago
0
sc3_plot_de_genes duplicate row names
#55
koelling
closed
6 years ago
2
Color changing of heatmap annotation (sc3_plot_consensus & expression, etc..)
#54
jy-nam
closed
6 years ago
4
'x' must be an array of at least two dimensions
#53
kieranrcampbell
closed
6 years ago
14
unable to generate sc3_plot_cluster_stability plot in loop
#52
ghost
closed
6 years ago
4
sc3(s) giving error
#51
galib36
closed
6 years ago
6
Problems with calculate_distance() and sc3_calc_dists() functions
#50
sozzznanie
closed
6 years ago
9
Replaced all SCESet with SingleCellExperiment
#49
Shians
closed
7 years ago
1
Is it safe to just replace all reference to SCESet with SingleCellExperiment?
#48
Shians
closed
6 years ago
2
Check random seed
#47
wikiselev
opened
7 years ago
7
sc3_plot_de_genes and sc3_plot_markers not working
#46
yicheinchang
closed
6 years ago
4
sc3_plot_silhouette generate an empty plot
#45
yicheinchang
closed
6 years ago
2
All genes were removed after the gene filter! Stopping now...
#44
neocaleb
closed
7 years ago
4
[suggestion]maybe it could be better just using the SingleCellExperiment class
#43
LuyiTian
closed
7 years ago
7
Loading SC3 in R 3.4.1
#42
harrydgnt
closed
7 years ago
2
column annotations and list of genes
#41
dkoppstein
closed
7 years ago
1
Error in silhouette.default(clusts, diss) : object 'sildist' not found
#40
tweirick
closed
7 years ago
2
sc3_plot_de_genes does not work
#39
yicheinchang
closed
7 years ago
6
compute time
#38
yuqiyuqitan
closed
7 years ago
4
Installation failed
#37
zhiyuanhu
closed
7 years ago
2
ubuntu 16.04 SC3 1.4.2 or 1.5.1 bugs
#36
weizhiting
closed
7 years ago
7
'sc3' is not a slot in class "SCESet"
#35
slowkow
closed
7 years ago
8
No 'dimnames' attribute for array
#34
JRWK
closed
7 years ago
2
Error running sc3() - Error in unserialize(socklist[[n]]) : error reading from connection
#33
Hoohm
closed
7 years ago
23
Change the default slot used to get expression values
#32
wikiselev
closed
8 years ago
1
Optimise sc3_biology_calc() by using Rccp
#31
wikiselev
opened
8 years ago
0
Add column colouring to sc3_plot_markers
#30
kieranrcampbell
closed
8 years ago
3
Reintroduce show.original.labels using the scater phenoData matrix
#29
wikiselev
closed
8 years ago
1
Added comments to cpp and corrected eskTW bound.
#28
ay2sanger
closed
8 years ago
0
Added k-estimation function
#27
ay2sanger
closed
8 years ago
0
Changes to transformations and test added.
#26
ay2sanger
closed
8 years ago
0
Spectral Transformation time improvement
#25
ay2sanger
closed
8 years ago
0
k-means parameters
#24
ay2sanger
closed
8 years ago
0
Fixed "Labels" and "Stability" tabs issues.
#23
ay2sanger
closed
8 years ago
0
SC3 Optimization changes
#22
ay2sanger
closed
8 years ago
0
Add and explain non-interactive analysis
#21
wikiselev
closed
8 years ago
5
Change GO analysis from Webgestalt to gProfiler
#20
wikiselev
closed
8 years ago
1
Cluster coverage feature
#19
wikiselev
closed
8 years ago
2
Add a total number of marker genes in each cluster to the labels on Marker genes plot
#18
wikiselev
closed
8 years ago
1
Add cell labels ordered by original labels in the export
#17
wikiselev
closed
8 years ago
1
Add text explanation to tabPanels
#16
wikiselev
closed
8 years ago
1
Move auroc.threshold parameter from sc3() to the UI
#15
wikiselev
closed
8 years ago
2
URGENT - add a download link for the consensus matrix
#14
wikiselev
closed
8 years ago
1
Add note in documentation about minimum java version requirement for RSelenium
#13
wikiselev
closed
8 years ago
1
make all columns in output tables numeric
#12
wikiselev
closed
8 years ago
1
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