niaid/dsb

Issues

• ## Advance use error

  #45 opened 5 months ago by Sogand65
  6

• Should we scale the data?

  #34 opened 2 years ago by fredust
  3

• DSB validity for limited ADT features

  #46 opened a year ago by saimaniharreddy
  1

• Selecting Cut-Off Value For ADT Expression

  #43 opened a year ago by codeneeded
  2

• Empty droplet definition with Mission Bio data

  #41 opened a year ago by mcortes-lopez
  4

• Integrated multiple samples

  #44 opened a year ago by Aaron-sqw
  1

• DSB with high throughput method

  #42 opened a year ago by ojbednar
  1

• Truncating negative values

  #39 opened a year ago by erflynn
  2

• ValueError (ill-defined empirical covariance)

  #35 opened 2 years ago by m21camby
  2

• Variation due to library size remains in normalized counts.

  #36 opened a year ago by Thapeachydude
  1

• (denoise.counts=TRUE, use.isotype.control=TRUE) very similar (denoise.counts=FALSE, use.isotype.control=FALSE)

  #37 opened a year ago by domi84
  1

• Do Isotype Control Values have to be Subtracted?

  #38 opened a year ago by codeneeded
  2

• choice of graph to use for clustering unclear?

  #40 opened a year ago by naila53
  1

• Additional normalization?

  #4 opened 5 years ago by yksaito
  2

• Not issue quickstart example plots

  #11 opened 4 years ago by MattPM
  0

• return.stats use-case error

  #32 opened 2 years ago by diegoalexespi
  2

• longer object length is not a multiple of shorter object length

  #31 opened 3 years ago by dtatarak
  3

• Question: Workflow using HTOdemux

  #30 opened 3 years ago by m3lorra
  4

• dsb package environment

  #28 opened 3 years ago by jjs847
  2

• CiteSeqCount on empty droplet whitelist

  #29 opened 3 years ago by EspressoKris
  11

• batch-effect correction in DSB-normalized data?

  #12 opened 4 years ago by massonix
  4

• Finding the right cutoffs manually

  #20 opened 3 years ago by ColeKeenum
  8

• Error in cells$`Gene Expression`

  #27 opened 3 years ago by rpauly
  5

• Integrating RNA+DSB using Seurats v4 WNN

  #13 opened 4 years ago by danmoore1987
  3

• Error in quantile.default

  #26 opened 3 years ago by gt7901b
  3

• differential expression analysis: log2FC on negative DSB-normalized values

  #23 opened 3 years ago by cyc2145
  9

• object 'count_prot' not found

  #25 opened 3 years ago by johaab
  2

• Log transform DSB-normalised corrected ADT counts

  #18 opened 3 years ago by jkniffka
  3

• DropletUtils::EmptyDrops?

  #17 opened 3 years ago by bbimber
  4

• multiplexing experiments section?

  #16 opened 3 years ago by bbimber
  1

• Quantile trimming after dsb normalisation

  #22 opened 3 years ago by mdmanurung
  2

• Filtering cells of multiplexed experiment stained with TotalSeq-A universal panel

  #21 opened 4 years ago by mdmanurung
  2

• DSB normalising with artificial (zero) background

  #19 opened 4 years ago by jkniffka
  1

• Adding a tag

  #15 opened 4 years ago by Accio
  4

• Decision tree for deciding whether to set denoise.counts = TRUE

  #14 opened 4 years ago by malisas
  2

• range of normalized values

  #9 opened 4 years ago by bio-la
  5

• as.matrix conversion: memory issues

  #10 opened 4 years ago by Daliya-K
  5

• AB isotypes needed?

  #7 opened 4 years ago by bio-la
  7

• Error in quantile.default(x, seq(from = 0, to = 1, length = n)) :

  #6 opened 4 years ago by naity
  3

• Using emptyDrops on RNA to define my negative matrix

  #8 opened 4 years ago by sorjuela
  3

• cellranger Vs CITE-seq-count

  #5 opened 5 years ago by sorjuela
  4

• isotype controls

  #2 opened 5 years ago by igordot
  2

• Advise without HTODemux

  #1 opened 5 years ago by sorjuela
  2