ImmuneDynamics/Spectre

Issues

• Experiment with different CI for master

  #184 opened 2 months ago by ghar1821
  1

• Adapting conversion of data.table to sce for input data.frame

  #193 opened 2 months ago by denvercal1234GitHub
  0

• Advice for automated cell classification workflow between datasets with different number of parameters

  #188 opened 5 months ago by denvercal1234GitHub
  6

• How to identify/visualize co-expression (correlation) between markers?

  #182 opened 9 months ago by WilliamMWei
  5

• Improve umap runtime

  #141 opened a year ago by ghar1821
  5

• Unable to download and install development version

  #186 opened 6 months ago by earbebarnes
  10

• Error in prep.cytonorm

  #179 opened 9 months ago by mortadelo93
  4

• Error in prep.cytonorm - Reading FCS files

  #153 opened 4 months ago by grizzly2207
  5

• Is skipping data transformation for channel values in Spectre workflow only is specific to the Spectre workflow?

  #150 opened 4 months ago by denvercal1234GitHub
  2

• Real or technical artifacts due to errors detected in UMAP following run.flowsom()?

  #161 opened 4 months ago by denvercal1234GitHub
  3

• Clustering datasets with >50 million cells

  #185 opened 4 months ago by AbbeyFigliomeni
  10

• Discovery workflow with batch alignment using CytoNorm -- link broken

  #189 opened 4 months ago by mariecrane
  4

• Exported channel values do not agree with what was shown in FlowJo Biex?

  #163 opened 4 months ago by denvercal1234GitHub
  8

• Advice on how to sub-cluster?

  #164 opened a year ago by denvercal1234GitHub
  8

• cannot install on an ARM mac

  #181 opened 9 months ago by chintanparekh2301
  4

• Problem with make.multi.plot.R

  #180 opened 9 months ago by markmelzer
  7

• The data Error: object 'merge.channels' not found in Ilastik Protocol.

  #175 opened 9 months ago by andreyevteev23
  2

• Error with prep.cytonorm

  #169 opened a year ago by MattCrossley99
  3

• Quantile error in make.colour.plot()

  #167 opened a year ago by jamesboot
  4

• transpose = T/F in make.pheatmap() produced inconsistent results

  #140 opened 2 years ago by denvercal1234GitHub
  3

• Error when running run.flowsom with meta.k set to 2

  #166 opened a year ago by jamesboot
  2

• Use here package to replace setwd in all functions

  #162 opened a year ago by ghar1821
  1

• Error installing dependency exactextractr

  #156 opened a year ago by jamesboot
  6

• No appropriate meta clustring with run.flowsom

  #154 opened a year ago by Tenrolf
  3

• Warning: Stopped early on line 498. Expected 2 fields but found 3. Consider fill=TRUE and comment.char=. First discarded non-empty line: <<$P9E,0,0>>

  #157 opened a year ago by denvercal1234GitHub
  1

• Error in is(d, "matrix") : object 'dat.bk' not found during Spectre::run.umap

  #155 opened a year ago by denvercal1234GitHub
  1

• How to identify and remove "bad/outlier" FCS files objectively, before performing clustering?

  #148 opened a year ago by denvercal1234GitHub
  4

• How to best use peacoQC() in Spectre workflow?

  #149 opened a year ago by denvercal1234GitHub
  8

• How to use a different cofactor for every channel in Spectre workflow?

  #147 opened a year ago by denvercal1234GitHub
  2

• Create a function argument to dictate the order in multi plots

  #151 opened 2 years ago by tomashhurst
  0

• Install problem for R version 4.2.1

  #142 opened 2 years ago by charlottedevries
  4

• Unable to install Spectre for RStudio Version 3.6.3

  #135 opened 2 years ago by jamila-griffith
  1

• Generating Summary Table

  #139 opened 2 years ago by jvazquez3
  2

• Maximum Number of Batches?

  #134 opened 2 years ago by ramziabb
  3

• Issue when running FlowSOM in Simple Discovery Workflow

  #138 opened 2 years ago by SamN01
  2

• error in prep.cytonorm

  #127 opened 2 years ago by domivf
  4

• write.hdf5: Error in quantile.default(over.one, 0.05), missing values

  #119 opened 3 years ago by mabar1
  3

• Error in multicut_2_segment

  #126 opened 2 years ago by adriadalmau
  0

• ‘simple’ discovery analysis workflow

  #125 opened 2 years ago by sailseem
  7

• write.hdf5: plot merged channel stored in AR?

  #120 opened 3 years ago by mabar1
  1

• write.files(cell.dat, i, write.csv = FALSE, write.fcs = TRUE)

  #105 opened 2 years ago by sailseem
  2

• where to follow the cellular and spatial analysis

  #106 opened 2 years ago by sailseem
  1

• truncate_max_range = FALSE

  #121 opened 2 years ago by dietmar113
  2

• Region analysis with 'NA's

  #117 opened 3 years ago by tomashhurst
  0

• Review the NA vs 0 metrics

  #118 opened 3 years ago by tomashhurst
  0

• Centroid label missing if the x and y range is < 1

  #116 opened 3 years ago by ghar1821
  3

• Unsuccessful installation of Spectre

  #113 opened 3 years ago by raquel-galfig
  3

• area analysis on DATA.TABLE

  #111 opened 3 years ago by Mark-Ste
  1

• advanced spatial, error in .local

  #107 opened 3 years ago by Mark-Ste
  1

• Why is always that the first cluster is not shown in umap? Missing values Warning

  #89 opened 3 years ago by denvercal1234GitHub
  4