benjjneb/decontam

Issues

• How to apply decontam to functional data

  #151 opened 3 months ago by Ivy-ops
  2

• Batch-specific contaminant detection or not?

  #150 opened 5 months ago by zztin
  0

• Importing dada2 output

  #149 opened 6 months ago by nadeaujay
  3

• Use of frequency-based decontam method on Meta-transcriptomics data

  #148 opened 6 months ago by achald7867
  0

• decontam use

  #147 opened 7 months ago by Zarzarn95
  3

• EPI2ME decontam Oxford nanopore sequencing

  #146 opened 9 months ago by CamillePhilippeSCI
  2

• Install issues

  #145 opened 9 months ago by acrowell09
  6

• Decontam error

  #143 opened 9 months ago by OluchiAroh
  4

• Can i use "frequency" without DNA concentration?

  #144 opened 10 months ago by kx11jkjk
  3

• DNA concentrations for half of the samples are 0.1ng/ul before PCR. Can I do decontam?

  #142 opened a year ago by sihanbu
  2

• Result vary as per sample size

  #140 opened a year ago by achald7867
  6

• Removal of contamination based on a negative control occurs when all of "P = NA"

  #141 opened a year ago by 1023011930
  16

• When are assumptions for decontam violated?

  #120 opened 2 years ago by pslai
  1

• Selection of methods for different sample types and non-subjective strategy to select method and threshold

  #139 opened a year ago by cBundg
  2

• Problems with the decontamination of metagenomic data or viral data

  #136 opened a year ago by 1023011930
  6

• Prevalence mode pruning

  #138 opened a year ago by skose82
  2

• Here more NAs exist inside the calculated P-value and are classified as FALSE (non-contaminated features).

  #133 opened 2 years ago by YMSen
  3

• a

  #137 opened a year ago by cafferychen777
  0

• Best way to use controls for multiple batches?

  #135 opened a year ago by DrLCode
  1

• Is one negative control useless for this application?

  #134 opened a year ago by lowrda
  2

• How to use controls in multiple small batches over one experiment

  #132 opened 2 years ago by AlexaBennett
  2

• very cross-contaminated samples

  #131 opened 2 years ago by lauraDRH
  6

• isContaminant with batch option

  #130 opened 2 years ago by Martinique-F
  2

• extraction control, pcr control and "buffer" control

  #129 opened 2 years ago by doloacu
  1

• Probable bug in "getFromPS(ps, conc) : ng.DNA is not a valid sample-variable in the provided phyloseq object."

  #128 opened 2 years ago by roey-angel
  2

• is "quant_reading" DNA concentration in some units or total DNA

  #127 opened 2 years ago by Rob-murphys
  5

• Negative control count best practices

  #126 opened 2 years ago by Rob-murphys
  3

• Can I use decontam with these data?

  #101 opened 3 years ago by lyonskvn
  7

• Strange prevalence plot contamination in controls

  #125 opened 2 years ago by ladywaspzhu
  1

• Positive control contamination

  #123 opened 2 years ago by FarzanehRah
  1

• p.freq differs when using method="frequency" and method="auto/combined/minimum/either/both"

  #122 opened 2 years ago by zz77zz
  1

• Very few contaminant detected regarding to the total number of ASVs

  #121 opened 2 years ago by Mcouedel
  1

• Export data from prevalent option

  #119 opened 2 years ago by K-Gutierrez
  2

• prevalence method figure; Prevalence (Negative Controls) on x-axis against Prevalence (True Samples) on y-axis?

  #108 opened 2 years ago by marwa38
  7

• Problems with "prune_taxa"

  #118 opened 2 years ago by Englittrigfisk
  1

• "Biological ASVs" identified as contaminants / "Contaminant ASVs" not identified as contaminants

  #117 opened 2 years ago by tellafiela
  2

• DNA concentration inputs

  #116 opened 2 years ago by devinjones18
  1

• Weird decontam performance

  #105 opened 3 years ago by Gian77
  13

• Importing the data

  #115 opened 2 years ago by lynneitelson
  7

• Error in data.frame and Removed 3 samples with zero total counts (or frequency)

  #114 opened 2 years ago by Paty-Azevedo
  4

• Controls Removal prior to filtering contaminants using 'frequency'

  #113 opened 3 years ago by andrebolerbarros
  3

• Used rarefided or unrarefided feature-table

  #112 opened 3 years ago by suiweikang
  3

• What is false contaminant?

  #111 opened 3 years ago by dikiprawisuda
  1

• Distribution of score statistics varies based on exclusion/inclusion of batch parameter

  #110 opened 3 years ago by starcutie
  0

• A LOT of contamination in controls

  #109 opened 3 years ago by sash2566
  1

• Methylobacterium-Methylorubrum as a contaminant, advice?

  #107 opened 3 years ago by marwa38
  3

• Where does quant_reading come from? Where does it go?

  #106 opened 3 years ago by pauGuas
  1

• Proposal - hierarchical approach

  #104 opened 3 years ago by andrewjmc
  2

• Didn't find contaminants how to proceed?

  #103 opened 3 years ago by JoaoMiranda96
  4

• Which is the right threshold value?

  #102 opened 3 years ago by Aliax3
  2