benjjneb decontam issues

benjjneb / decontam

Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

https://benjjneb.github.io/decontam/

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issues

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Proposal - hierarchical approach

#104 andrewjmc closed 3 years ago
2
Didn't find contaminants how to proceed?

#103 JoaoMiranda96 opened 3 years ago
4
Which is the right threshold value?

#102 Aliax3 closed 3 years ago
2
Can I use decontam with these data?

#101 lyonskvn opened 3 years ago
7
Features(ASVs) found in negative controls only not identified as contaminants

#100 ibrila closed 3 years ago
3
microbiome decontamination

#99 antoine4ucsd opened 3 years ago
2
probable bug plot_frequency

#98 wsteenhu opened 3 years ago
0
Removing zeroes

#97 andrewjmc closed 3 years ago
2
How many control samples?

#96 vfonti opened 3 years ago
1
What is considered as a batch?

#95 biomarv opened 3 years ago
1
ENH: thoughts on supporting sparse data?

#94 mortonjt opened 3 years ago
2
Using quantile-quantile plots to identify threshold values (question and suggestion for documentation enhancement)

#93 JacobRPrice opened 3 years ago
0
Using {decontam} with two target markers

#92 mxdub opened 3 years ago
1
The best threshold and other questions about Decontam

#91 kla44 opened 3 years ago
1
all FALSE

#90 wangqiqi1995 opened 3 years ago
5
enabling S4 dispatch for main functions

#89 FelixErnst closed 3 years ago
5
Including controls in frequency method, principle behind the combination method & different types of controls

#88 LoreVE closed 3 years ago
5
Example analysis on published oral mucosal dataset

#87 Ziggsblitz opened 3 years ago
1
2x2 presence/absence table

#86 younjungkim0513 closed 3 years ago
3
Positive controls and decontam (reposting issue #83)

#85 tiagojp opened 3 years ago
4
DNA concentrations and two-step PCR

#84 smonteux closed 3 years ago
2
Positive controls and decontam

#83 tiagojp opened 4 years ago
0
Decontam question

#82 mcavoytj opened 4 years ago
4
Cell-line negative controls

#81 chrisquatjr opened 4 years ago
2
no TRUE

#80 JMBookw opened 4 years ago
6
Clarification on Batch.combine and when to use certain parameters

#79 hbussan closed 4 years ago
2
Some batches contain zero or one samples.

#78 nhg12 opened 4 years ago
8
Fix word mistake in decontam_intro.Rmd

#77 mikemc closed 4 years ago
0
Error when pruning samples to make Prevalence map

#76 hbussan opened 4 years ago
2
Error using 'decontam'

#75 ziabulous-repository opened 4 years ago
17
Understanding NA scores and filtering requirements

#74 HSapers opened 4 years ago
3
Specifying multiple confounders for batch parameter

#73 cdeanj closed 4 years ago
1
Reading in data as a phyloseq object using readRDS()

#72 NaomiHuntley opened 4 years ago
5
Amplicon sequencing : decontam

#71 tabaresr opened 4 years ago
4
Distribution of scores assigned by decontam

#70 cdeanj closed 4 years ago
3
Adjusting the false discovery rate in frequency mode

#69 nickilott closed 4 years ago
3
Choice of threshold

#68 jw51 closed 4 years ago
7
Quant values to be used: assay or stock calculation(QuBit)?

#67 emilyjunkins closed 4 years ago
2
Write.csv of contaminants and removing by ASV #

#66 miakeady opened 5 years ago
3
plotting contaminant frequencies and sample dna concentrations for multiple otus

#65 mmvivaldi closed 5 years ago
9
Three different types of controls

#64 Jasmine84 opened 5 years ago
9
Usage clarification of isContaminant and isNotContaminant

#63 Ziggsblitz opened 5 years ago
3
Plot_frequency y-axis

#62 miakeady closed 5 years ago
4
Paired samples running Decontam and how to extract ASV/map ASV to taxtable

#61 Jasmine84 opened 5 years ago
5
Syntax issue on paragraph 05

#60 kant closed 5 years ago
1
isNotContaminant example in reference manual

#59 ScaonE opened 5 years ago
2
plot_frequency error

#58 lixiaopi1985 opened 5 years ago
1
Working with low bio mass placental samples

#57 toluayo opened 5 years ago
9
Difference between IsContaminant and isNotContaminant

#56 Jewelna opened 5 years ago
4
Negative controls not separating out

#55 hpremathilake opened 5 years ago
2

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