SingleR-inc/SingleR

Issues

• Speed issue with SingleR v2.8.0 in BioC 3.20

  #292 opened 16 days ago by ycl6
  4

• cannot use de.method="wilcox" and plotMarkerHeatmap function.

  #291 opened 21 days ago by AmmyDK
  1

• Simplify `combineRecomputedResults` scores into a nested DF of DFs

  #290 opened a month ago by LTLA
  1

• Switch to beachmat's `row_nan_counts()` for NA removal.

  #289 opened a month ago by LTLA
  1

• Throw an error if there are duplicate rownames in the reference

  #287 opened a month ago by LTLA
  2

• Separate `check.missing=` arguments for test and reference datasets

  #288 opened a month ago by LTLA
  0

• object of type 'S4' is not subsettable

  #286 opened 2 months ago by robertzeibich
  2

• Extracting cell-annotated genes

  #285 opened 2 months ago by wenxiang688
  6

• test and ref in the function SingleR

  #284 opened 2 months ago by jianhaizhang
  2

• Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE. Traceback:

  #268 opened 8 months ago by ArzooShamoon
  5

• Split conditions and annotate

  #278 opened 2 months ago by feanaros
  3

• Can SingleR work with a Xenium object?

  #280 opened 2 months ago by jbrandst7
  1

• Migrate internal dependences from scran to scrapper

  #282 opened 2 months ago by LTLA
  0

• Create a `plotMarkerHeatmap` function

  #281 opened 3 months ago by LTLA
  1

• SingleR book site not found

  #251 opened 3 months ago by Lucyyang1991
  3

• Bioc devel version: Expecting an external pointer: [type=list]

  #279 opened 3 months ago by bbimber
  5

• Fix some plot-related warnings in the tests

  #276 opened 4 months ago by LTLA
  2

• Error in is.null(rownames(x)) && nrow(x) : invalid 'y' type in 'x && y' only on ImmGen data.

  #269 opened 8 months ago by aleferna
  3

• Validity of SingleR with very small bulk RNAseq reference

  #273 opened 6 months ago by nickhir
  2

• ifnb@assays$SCT$data, ifnb@assays$RNA$data

  #272 opened 6 months ago by zznx
  4

• SingleR: download Error

  #270 opened 8 months ago by isaiao01
  5

• SingleR - "sc_data" is missing

  #265 opened 8 months ago by nitinmahajan20
  1

• SingleR: GetAssayData doesn't work for multiple layers in v5 assay

  #266 opened 8 months ago by Eos-halo
  1

• Can we use Bulk Time-series datasets to annotate other bulk RNA samples

  #267 opened 9 months ago by Rohit-Satyam
  1

• singleR runs forever

  #264 opened a year ago by ryanhchung
  1

• Pruned labels doubts

  #262 opened a year ago by MartaBenegas
  6

• "object of type 'S4' is not subsettable" error

  #263 opened a year ago by ycl6
  2

• Installation of SingleR in R/4.2.2 using BiocManager v3.16 fails

  #260 opened a year ago by star0044
  1

• Annotation of integrated counts

  #257 opened a year ago by LeaLe88
  2

• Error： no common genes between 'test' and 'ref'

  #258 opened a year ago by MOKA1066
  1

• fatal error: Rtatami.h: No such file or directory

  #249 opened a year ago by ramadatta
  2

• JoinLayers function for Seurat Object for annotation with SingleR

  #254 opened a year ago by LeaLe88
  4

• Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.

  #256 opened a year ago by LeaLe88
  5

• Error: useNames = NA is defunct. Instead, specify either useNames = TRUE or useNames = FALSE.

  #255 opened a year ago by LeaLe88
  0

• error when running SingleR

  #252 opened a year ago by joe-jhou2
  4

• Cell Type abbreviation of ImmGenData

  #253 opened a year ago by Jammm11
  3

• Dealing with underrepresented cell types across references

  #250 opened a year ago by samgest
  1

• SingleR: did not converge in 10 iterations

  #248 opened a year ago by abulislam
  0

• Is it appropriate to use RNAseq data to annotate flow cytometry data via SingleR?

  #246 opened a year ago by denvercal1234GitHub
  4

• Example of using harmonised labels for `de.method="wilcox"` instead of classic marker detection

  #247 opened a year ago by denvercal1234GitHub
  1

• could not find function "CreateSinglerObject"

  #245 opened a year ago by coconutll
  1

• BiocParallel errors：could not find function ".OLD_read_block"

  #244 opened a year ago by alopehba
  3

• Should `trainSingleR()` make use of log-transformed P-values?

  #241 opened 2 years ago by PeteHaitch
  3

• BiocParallel errors

  #233 opened 2 years ago by antoine4ucsd
  12

• runtime for SingleR

  #239 opened 2 years ago by gebdu
  1

• Library loading issue

  #238 opened 2 years ago by rytpark
  1

• Infinite execution when multithreading is enabled

  #237 opened 2 years ago by ATpoint
  4

• Vignette Doesn't Explore Between-Atlas Labelling Stability

  #236 opened 2 years ago by DarioS
  2

• `error: call of overloaded 'XPtr(Rcpp::Vector<19>::Proxy)' is ambiguous` during installation.

  #232 opened 2 years ago by jxshi
  1

• Viewing the classification genes

  #234 opened 2 years ago by antoine4ucsd
  7