ncborcherding scRepertoire issues

ncborcherding / scRepertoire

A toolkit for single-cell immune profiling

https://www.borch.dev/uploads/screpertoire/

MIT License

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issues

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Renaming cells of seurat object to match those for scRepertoire

#400 zoqaiyum closed 3 months ago
3
[question] Comparsion of the "same" clones btwn samples

#399 jinhys closed 1 month ago
2
could not find function "quantContig"

#398 Lingxuewang closed 3 months ago
2
v2.0.5

#397 ncborcherding closed 3 months ago
0
New cloneCall option to more closely match `immunarch` options?

#396 jeremymsimon closed 1 month ago
5
Clarification regarding (1) the output of differential enrichment of enrichment scores and (2) negative enrichment scores

#395 denvercal1234GitHub closed 3 months ago
3
How to Assess Clonal Diversity at the Subgroup Level?

#394 lisch7 closed 3 months ago
8
small quality of life changes with assertthat

#393 Qile0317 closed 3 months ago
0
V2.0.4: could not find function "clonalQuant"

#392 yujuanGG closed 4 months ago
1
How to map barcode of scTCRseq and scRNAseq

#391 synatkeamsk closed 4 months ago
3
combineExpression for chain='TRB' error 'full.clone' not found

#390 EeSsSs closed 4 months ago
4
runEscape - subscript out of bounds error

#389 kkearns13 closed 4 months ago
3
Duplicate barcodes

#388 carlares closed 3 weeks ago
4
Functions not working

#387 sumanta-barman closed 4 months ago
2
Issue with clonalNetwork plot

#386 Xili0426 closed 4 months ago
2
Re-importing CSV file

#385 HRSharpe closed 5 months ago
2
clonalCluster - edge.list[, 1]

#384 MariusMathies closed 5 months ago
5
clonalNetwork

#383 Anikagir closed 5 months ago
1
Make hyperexpanded clones appears clearly and big/large

#382 synatkeamsk closed 5 months ago
1
How to specify colors for the clusters in `clonalOverlay` UMAP?

#381 denvercal1234GitHub closed 5 months ago
1
Question : compareClonotypes output >number of top clones

#380 paulrbuckley-kcl closed 5 months ago
1
what is the proportion(y axis) in compareClonotypes() function?

#379 ilovegreentea closed 5 months ago
1
Understand difference of NA and none in BCR sequence

#378 MariusMathies closed 5 months ago
2
Understand difference of NA and none in BCR sequence

#377 MariusMathies closed 5 months ago
0
Unexpected behaviour of `filter.graph` in `clonalNetwork`?

#376 denvercal1234GitHub closed 5 months ago
1
Incomplete merging of vdj data and seurat with combineExpression function

#375 cnwokolo24 closed 5 months ago
0
Question about alluvialClones

#374 feather-W closed 5 months ago
0
Error in combineTCR(contig.list, samples = "Pt17", cells = "T-AB", filterMulti = TRUE, : unused argument (cells = "T-AB")

#373 yueli8 closed 6 months ago
1
v2.0.4

#372 ncborcherding closed 6 months ago
0
runEscape: unable to find an inherited method for function 'gsva' for signature '"missing", "missing"'

#371 Diennguyen8290 closed 6 months ago
5
positionalProperty Error in propertyFunc[char, ] : subscript out of bounds

#370 yueli8 closed 6 months ago
3
Regular expression used for quietTCRgenes.R

#369 user-pagh closed 6 months ago
1
Error in apply(strings, 2, function(z) { : dim(X) must have a positive length

#368 monikaramos closed 6 months ago
0
Error in hclust(as.dist(distances), method = method) : NA/NaN/Inf in foreign function call (arg 10)

#367 yueli8 closed 6 months ago
3
Error in propertyFunc[char, ] : subscript out of bounds

#366 yueli8 closed 6 months ago
4
Specifics of clonalQuant()

#365 kriegerm closed 6 months ago
7
convert MiXCR format to scRepertoire format: Error in `df[[i]][, c(1, 2, 20, 25, 30, 35, 48, 49, 4)]` undefined columns selected

#364 yueli8 closed 6 months ago
2
retaining labels from clonalCompare(relabel.clones=TRUE)

#363 kriegerm closed 6 months ago
2
dev level with master for v2.0.3 onward

#362 ncborcherding closed 6 months ago
0
The Github version and Bioconductor version differ

#361 llrs closed 6 months ago
2
plotUMAP(sce, colour_by = "cloneSize") : could not find function "plotUMAP"

#360 hangsuUNC closed 6 months ago
1
v2.0.3

#359 ncborcherding closed 6 months ago
1
Issue Merging Seurat Data with the Combined TCR Object

#358 ghoeltzel38 closed 6 months ago
9
group.by ordering for visualizations

#357 ncborcherding closed 6 months ago
1
could not find function "parseAIRR"

#356 kriegerm closed 7 months ago
18
combineTCR v/d/j/c_gene

#355 jakob-arnold closed 7 months ago
6
Issue with "group.by" for clonalOverlap

#354 sc30301 closed 7 months ago
4
Clonality matrix under scRepertoire

#353 synatkeamsk closed 7 months ago
6
Clonal overlap

#352 Sogand65 closed 7 months ago
4
Update Ibex/Trex vingette

#351 ncborcherding closed 7 months ago
0

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