hemberg-lab/SC3

Issues

• Question about <NA> labels from cell clustering via SC3

  #111 opened 8 months ago by yxy92
  1

• could not find function "calculate_distance"

  #108 opened 2 years ago by irtisha
  2

• sc3_run_svm has a prediction issue

  #110 opened a year ago by jmuribes
  2

• Running SC3 in integrated data

  #109 opened 2 years ago by anemartinezlarrinaga2898
  1

• Error in `[.default`(clusts, , paste0("sc3_", hash.table[i, 1], "_clusters"))

  #73 opened 6 years ago by DrLucyMac
  10

• Error in prcomp.default

  #97 opened 5 years ago by dsimps1993
  4

• one node produced an error: Error in ED2(data)

  #103 opened 3 years ago by eshraaqsaeed
  1

• long vectors are not supported in .C

  #107 opened 3 years ago by zhangtongda
  1

• Saving SC3 clustering output as csv files

  #106 opened 3 years ago by bsamal20
  3

• saving SC3 output

  #105 opened 3 years ago by bsamal20
  0

• Consider using Forks for parallelism?

  #83 opened 3 years ago by Shians
  3

• The Perl script 'WriteXLS.pl' failed to run successfully.

  #102 opened 4 years ago by UnkownNames
  0

• No gene names in export results

  #87 opened 6 years ago by dsimps1993
  4

• Error in rowSums(out_pathway) : 'x' must be an array of at least two dimensions

  #101 opened 4 years ago by zina-R
  1

• sc3_kmeans produces "Warning message: Quick-TRANSfer stage steps exceeded maximum (= 250000)"

  #100 opened 4 years ago by MikeHala
  1

• Which remove-batch-effect package work best with SC3?

  #99 opened 4 years ago by kuang-da
  1

• Sparse matrix causes errors

  #98 opened 5 years ago by RebekkaWegmann
  2

• each element of 'reducedDims' must be a matrix-like object with nrow equal to 'ncol(object)

  #96 opened 5 years ago by makimenkova
  1

• sc3_plot_de_genes and sc3_plot_markers problems

  #84 opened 6 years ago by Santos22903
  2

• Gene names lost after get_marker_genes()

  #95 opened 5 years ago by friedue
  0

• Large number of NA's when run on large dataset.

  #68 opened 6 years ago by TChan92
  17

• Plot expression on given list of genes

  #94 opened 5 years ago by shabs24
  1

• Clustering for more than 10000 Genes

  #93 opened 5 years ago by hkarakurt8742
  3

• SC3 with Batch Correction

  #92 opened 5 years ago by hkarakurt8742
  1

• How to calculate D?

  #91 opened 5 years ago by XiHuYan
  4

• Which data type for clustering

  #85 opened 5 years ago by mkrzak
  2

• is it possible to surpress the message in `sc3` function.

  #82 opened 6 years ago by LuyiTian
  1

• error running sc3_plot_de_genes

  #88 opened 6 years ago by qiaowei-vvjoe
  8

• SC3 error on linux server: Not compatible with requested type

  #86 opened 6 years ago by LuyiTian
  5

• Error in ED2(data)

  #64 opened 6 years ago by biosyssun
  3

• Error in checkForRemoteErrors(val) :

  #72 opened 6 years ago by 15084921898
  2

• show_pdata errors in sc3_plot_expression(), sc3_plot_de_genes(), sc3_plot_markers(), but not sc3_plot_consensus()

  #65 opened 6 years ago by KeelyDulmage
  4

• Feature request: option to specify assay used

  #66 opened 6 years ago by dkoppstein
  5

• Excluding principal components from clustering

  #71 opened 6 years ago by martabrozynska
  2

• Not clear how SC3 exactly works

  #75 opened 6 years ago by CodeInTheSkies
  5

• SC3 repeatedly loads packages while running and has data display issues

  #76 opened 6 years ago by jamesrhowe
  3

• Small suggestion for sc3_prepare() documentation

  #80 opened 6 years ago by PeteHaitch
  1

• #UMI counts table

  #81 opened 6 years ago by penglbio
  1

• Plot column names

  #79 opened 6 years ago by simone-rizzetto
  1

• Specify custom genes/features

  #78 opened 6 years ago by royfrancis
  1

• Clusters for max 5000 cells

  #77 opened 6 years ago by julien-roux
  2

• first error: Error in transf[, 1:hash.table$n_dim[i]] : incorrect number of dimensions

  #61 opened 7 years ago by Jayjay601
  15

• Error in checkForRemoteErrors(val) : 3 nodes produced errors; first error: Error in ED2(data) : Not compatible with requested type: [type=S4; target=double].

  #74 opened 6 years ago by JesusCorria
  2

• Annotation colour palette in heatmaps

  #70 opened 6 years ago by wikiselev
  0

• k_estimator output not passed to sc3 wrapper function

  #67 opened 6 years ago by leonfodoulian
  1

• sc3_plot_de_genes duplicate row names

  #55 opened 7 years ago by koelling
  2

• Error in !isSpike(object) : invalid argument type

  #59 opened 7 years ago by yicheinchang
  3

• default for `n_cores`

  #63 opened 7 years ago by stephaniehicks
  1

• export plot from SC3

  #62 opened 7 years ago by MichaelPeibo
  2

• Is there a way to pull out the stability index matrix from the SC3 object?

  #60 opened 7 years ago by yingzhang121
  7