YosefLab/scone

Issues

• BiocParallel Errors

  #107 opened 3 years ago by TeodoraTockovska
  2

• CellRanger Metrics

  #106 opened 3 years ago by CisnerosFernandez
  0

• Cell Ranger alignment stats

  #104 opened 4 years ago by iwillham
  3

• QC matrix

  #105 opened 3 years ago by HaniJieunKim
  0

• Calling scone with run=TRUE Error

  #102 opened 5 years ago by e-arslan
  1

• scran "sizes" parameter

  #86 opened 7 years ago by drisso
  4

• Deprecated inbuilt datasets for scRNAseq package used in Introduction to SCONE

  #103 opened 5 years ago by biancamocanu
  2

• Error in get_normalized due to no imputation / return_norm = "no"

  #101 opened 6 years ago by diyadas
  3

• Error with memory

  #100 opened 6 years ago by jgarces02
  0

• Error in score_matrix(expr = adjusted, eval_pcs = eval_pcs, eval_proj = eval_proj, : NA/Inf/NaN Expression Values

  #99 opened 6 years ago by diyadas
  0

• BiocParallel error in scone(run=TRUE): attempt to apply non-function

  #98 opened 6 years ago by aarzalluz
  8

• House keeping genes

  #97 opened 6 years ago by emmanuelsapin
  1

• friendly error message when negcon params are all FALSE

  #96 opened 6 years ago by allonw
  0

• log = TRUE option for get_normalized returns the natural log?

  #95 opened 6 years ago by cypranowska
  2

• 'k' must satisfy 0 < k < min(nrow(A), ncol(A))

  #93 opened 6 years ago by mbcole
  0

• bplapply memory issue when running scone(run=TRUE)

  #69 opened 8 years ago by ckmah
  3

• sconeReport

  #92 opened 7 years ago by mbcole
  0

• R-squared

  #91 opened 7 years ago by drisso
  1

• Add Helpful Message when Control Gene Lists are Malformed

  #90 opened 7 years ago by mbcole
  0

• Too many dependencies?

  #88 opened 7 years ago by drisso
  1

• ezbake error when fnr_maxiter = 0

  #87 opened 7 years ago by allonw
  0

• Warning when using default zero option

  #85 opened 7 years ago by drisso
  0

• Add wrapper for scran

  #70 opened 7 years ago by drisso
  4

• Scaling Function Arguments

  #84 opened 7 years ago by mbcole
  0

• Error is cryptic when row (gene) variance is 0

  #80 opened 7 years ago by deto
  1

• Add wrapper for total count normalization

  #82 opened 7 years ago by drisso
  1

• Factor Sample Filter Bug

  #81 opened 7 years ago by mbcole
  1

• SconeExperiment for signature matrix should accept character vectors for poscon and negcon

  #83 opened 7 years ago by drisso
  0

• Export get_bio() and get_batch()

  #78 opened 7 years ago by drisso
  2

• Report fails when expression feature is constant

  #79 opened 7 years ago by mbcole
  0

• packages httpuv and digest not installed with dependencies

  #60 opened 8 years ago by allonw
  19

• Scone not working on R 3.3.2 on MacOS

  #77 opened 8 years ago by festeneam
  4

• Stabilize simple imputation for use in primary experiments

  #55 opened 8 years ago by mbcole
  1

• Fix SCONE Script

  #74 opened 8 years ago by mbcole
  0

• Update sconeReport arguments for compatibility with S4

  #75 opened 8 years ago by mbcole
  0

• Memory issues with parallel computing

  #76 opened 8 years ago by drisso
  0

• POTENTIAL BUG: bplapply() and globals

  #57 opened 8 years ago by HenrikBengtsson
  5

• allow non-default BPPARAM

  #62 opened 8 years ago by allonw
  1

• select_methods does not subset score matrices

  #72 opened 8 years ago by mbcole
  1

• Allow multiple covariates

  #67 opened 8 years ago by drisso
  3

• Additional tests

  #71 opened 8 years ago by drisso
  0

• S4 Interface for SCONE

  #58 opened 8 years ago by mbcole
  2

• Run 4 data sets to evaluate imputation viability / moving ahead

  #56 opened 8 years ago by mbcole
  1

• Correct for QC and RUV simultaneously

  #68 opened 8 years ago by drisso
  0

• Report Design

  #59 opened 8 years ago by mbcole
  1

• sample filter: default hard cutoffs

  #66 opened 8 years ago by allonw
  0

• bug in scone_eval

  #65 opened 8 years ago by allonw
  1

• bug in easy bake

  #64 opened 8 years ago by allonw
  1

• exception in easybake

  #63 opened 8 years ago by allonw
  1

• metric_sample_filter interface not backwards compatible?

  #61 opened 8 years ago by allonw
  1