cole-trapnell-lab garnett issues

cole-trapnell-lab / garnett

Automated cell type classification

MIT License

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issues

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Problem Description:As of igraph version 2.1.0, the outnei() function has been officially removed and replaced with .outnei().

#70 doczhangt opened 1 week ago
0
classify_cells breaks with igraph 2.1.0

#69 const-ae opened 3 weeks ago
0
check_markers function using each cell as a different cell type

#68 hd4git opened 3 months ago
3
Cross-species comparative transcriptome analysis

#67 Geryxu08 closed 7 months ago
0
Regeneration Classifier

#66 neurohugo opened 1 year ago
4
Error in Creating CDS object for Garnett with Monocle 3: (Error: is(object = cds, class2 = "CellDataSet") is not TRUE)

#65 marwaabdelazim closed 1 year ago
1
Predicting Cell Type in VISIUM samples

#64 justinesjw closed 1 year ago
0
Unable to download package

#63 xu15825503775 closed 2 months ago
4
Checking my markers for upcoming "Training my own classifier" steps

#62 techgirl2022 closed 2 years ago
4
Run time to train new classifier

#61 lwtan90 closed 1 year ago
2
Marker list complexity for Garnett classifier

#60 hbandukw closed 2 years ago
1
Getting started with Garnett

#59 mommymisato closed 2 years ago
2
all cells are classified as UNKNOWN

#58 zh-zhang1984 closed 2 years ago
2
Force assignment to all cells?

#57 igrabski closed 2 years ago
2
Problem with sci-ATAC-seq analysis

#56 nbxszby416 closed 2 years ago
2
Changing cluster_extend_max_frac_unknown and cluster_extend=TRUE not results in less unknown

#55 keithgmitchell closed 3 years ago
2
"Error: is(object = cds, class2 = "CellDataSet") is not TRUE" & Prediction of large amount of "Unknown"

#54 nbxszby416 closed 3 years ago
6
Cannot find more nearest neighbours than there are points

#53 mahermassoud closed 4 years ago
1
Classifier Questions

#52 AlexCocker closed 3 years ago
2
Test Garnett with custom marker file

#51 zznx closed 4 years ago
1
Error in adjacent_vertices(x, i, mode = if (directed) "out" else "all")

#50 EleonoraLusito closed 3 years ago
2
<simpleError: 'coef.cv.glmnet' is not an exported object from 'namespace:glmnet'>

#49 evenDDDDD closed 4 years ago
3
Syntax error '(' at or near line when running check_markers()

#48 a-solovyev12 closed 4 years ago
2
train_cell_classifier getting stuck with no error

#47 dmiyagi closed 4 years ago
1
Wrong classification pattern depending on one marker

#46 EliseAld closed 4 years ago
2
Getting problems with marker free classifier for garnett.

#45 smk5g5 closed 4 years ago
4
Cell Type Similarity

#44 justinesjw closed 4 years ago
2
Trouble creating my own classifier

#43 smk5g5 closed 4 years ago
2
simpleError: 'coef.cv.glmnet' is not an exported object from 'namespace:glmnet'

#42 vswarup closed 4 years ago
2
Cluster extend possible issue

#41 lwhitmore closed 4 years ago
5
Fly genes

#40 hpliner closed 4 years ago
0
Error: Path '' does not exist train_cell_classifier

#39 liliay closed 4 years ago
2
garnett_check_markers not working for Fly

#38 dweemx closed 4 years ago
4
Garnett Installtion Error

#37 pbpayal closed 4 years ago
1
Garnett cluster graphs

#36 lwhitmore closed 4 years ago
1
installation using github file fails with error due to R version in which VGAM was built...

#35 SathiyaNManivannan closed 4 years ago
2
Not enough training samples for any cell types at the root of cell type hierarchy

#34 saisomesh2594 closed 4 years ago
2
cross species cell type transfer

#33 justinesjw closed 4 years ago
3
<simpleError: 'coef.cv.glmnet' is not an exported object from 'namespace:glmnet'>

#32 yejg2017 closed 4 years ago
5
Potential bug in implementation of tfidf

#31 VPetukhov closed 5 years ago
5
No constraints on cell type hierarchy during assignment

#30 VPetukhov closed 5 years ago
2
Option return_by_levels for classify_cells

#29 VPetukhov closed 5 years ago
1
Document return_initial_assign

#28 hpliner opened 5 years ago
0
Allow to extract assignment from all classification levels

#27 VPetukhov opened 5 years ago
4
Error in classify_cells: object 'excluded_cells' not found

#26 VPetukhov closed 5 years ago
1
build classifier on pre-labelled data

#25 hpliner closed 4 years ago
0
Classifier training issue

#24 jentiger82 closed 4 years ago
2
Setting cell type as subtype of self causes check_markers to hang

#23 RobertAlpin closed 5 years ago
1
bug in get_feature_genes() function

#22 a-solovyev12 closed 5 years ago
4
classifier for Linnarson brain cell type

#21 hhhcce closed 5 years ago
1