Discussions

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  Is it necessary to filter gene or cell filter needed after DecontX

  MISAKA-DaYu asked Apr 19, 2023 in Q&A · Unanswered

  

  

  

  

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  decontX not reproducible?

  trnguyenuka asked Sep 3, 2022 in Q&A · Unanswered

  

  

  

  

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  Does decontx support 10x HT samples? How to adjust delta for HT samples?

  MeshifLu started Jul 6, 2023 in General

  

  

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  Disagreement in contamination estimations with/without raw data

  dlee598 asked Apr 17, 2023 in Q&A · Unanswered

  

  

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  How to get the actual names of genes in celda

  markddesimone started Jan 31, 2023 in General

  

  

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  Decontx clusterstering looks weird for libraries which might affect analysis

  lquin003 started Nov 17, 2022 in General

  

  

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  High level of estimated contamination for same sample but different set of filtered cells

  dlee598 asked Nov 25, 2022 in Q&A · Unanswered

  

  

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  using decontx with filtered or raw matrix?

  dm8000 asked Aug 1, 2022 in Q&A · Unanswered

  

  

  

  

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  Decontx: Heuristic clustering or z parameter? How are the cluster labels specified with the z parameter affecting the decontamination?

  MartaSanchezCarbonell asked Aug 31, 2022 in Q&A · Answered

  

  

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  Formatting the count matrix to 10x feature barcode matrix HDF5

  shregeno8 asked Sep 13, 2022 in Q&A · Answered

  

  

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  Getting percentages of contamination

  sameehan2301 asked Jun 23, 2022 in Q&A · Unanswered

  

  

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  different genes

  wbf520qcp asked Jun 23, 2022 in Q&A · Answered

  

  

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  Using DecontX

  barbarashih asked Apr 19, 2022 in Q&A · Unanswered

  

  

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  Unexpected behavior when subsetting on decontaminated counts

  jmodlis asked Apr 4, 2022 in Q&A · Unanswered

  

  

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  cells with 100% contamination?

  plijnzaad asked Mar 20, 2022 in Q&A · Unanswered

  

  

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  Use of background argument

  Domoun asked Jan 19, 2022 in Q&A · Unanswered

  

  

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  Threshold to filter contaminated cells

  supermegamio asked Jan 11, 2022 in Q&A · Unanswered

  

  

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  Error in ‘reducedDim’ for UMAP

  karlaarz asked Oct 18, 2021 in Q&A · Answered

  

  

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  use of decontXcounts in subseq

  Sa753 asked Sep 1, 2021 in Q&A · Unanswered

  

  

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  using decontX on combined object, or on each sample individually?

  gruensch started May 3, 2021 in General

  

  

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  Sequencing depth corrected counts

  faraz89 asked Jan 13, 2021 in Q&A · Unanswered

  

  

  

  

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  is deconttX over correct my data

  mbourgey asked Dec 8, 2020 in Q&A · Unanswered

  

  

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  Can DecontX be used for scATAC-seq data ?

  dweemx asked Nov 12, 2020 in Q&A · Closed · Answered

  

  

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