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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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input matrix
#54
MjelleLab
closed
5 years ago
4
Deciding on "negatives" from field-collected samples
#53
rjoakim
opened
5 years ago
1
No true hits?
#52
ghost
opened
5 years ago
5
please delete question
#51
devonorourke
closed
5 years ago
0
Decontam with extremely low biomass samples
#50
liisaveerus
opened
5 years ago
5
isNotContaminant
#49
bmillerlab
closed
5 years ago
3
Contaminants sequence order
#48
sfeds
closed
4 years ago
5
Going back to qiime2 with Decontam output
#47
bmillerlab
closed
5 years ago
1
Which specimens to include in analysis
#46
tellafiela
opened
5 years ago
3
Input of isContaminant(): relative or absolute count table of ASVs/OTUs?
#45
antonioggsousa
closed
5 years ago
5
Low bacterial biomass and several batches
#44
luhugerth
opened
5 years ago
3
Regarding DNA quantitation data
#43
kotaarima
opened
5 years ago
7
Decontam by group necessary?
#42
sachasuca
opened
5 years ago
2
decontam removing ASVs of potential importance?
#41
EmmaDietrich
opened
5 years ago
9
Removing contaminants from samples
#40
msnyder424
opened
5 years ago
1
fix readme typos
#39
nbokulich
closed
5 years ago
0
Decontam w/ just one control?
#38
andrebolerbarros
closed
5 years ago
2
Questions by use concentration DNA
#37
molboss
opened
5 years ago
2
isContaminant - conc must be positive numeric
#36
chrstraub
opened
5 years ago
4
NA value when using either or both method
#35
llrs
opened
6 years ago
1
Allow blank samples
#34
llrs
closed
6 years ago
4
Optimal data for the frequency method?
#33
mniku
opened
6 years ago
4
Logic of the prevalence based method
#32
mniku
opened
6 years ago
6
Selection of negative controls and biological specimens
#31
tellafiela
opened
6 years ago
1
plot_frequency error
#30
sfeds
closed
6 years ago
11
How is presence/absence determined?
#29
zefrieira
closed
6 years ago
3
Request: visualization of probabilities used for classification
#28
elzerac
closed
6 years ago
2
error using isContaminant using prevalence and defining batch
#27
RimaChakaroun
closed
6 years ago
6
I think an additional method of filtering is needed
#26
waleadebayo
opened
6 years ago
8
Guidance when most samples are below detection limit
#25
benjjneb
opened
6 years ago
0
Clarification on DNA quantitation
#24
cyklee
closed
6 years ago
2
Using decontam to adjust taxonomic abundances based on taxa present in negative control
#23
smalanmul
closed
6 years ago
6
Install in R session
#22
johnchase
closed
6 years ago
1
Subtract prevalence values from samples?
#21
rachaelantwis
closed
6 years ago
4
Different kinds of negative controls
#20
casett
closed
6 years ago
2
correcting prevalence for read mis-assignment
#19
nhoffman
closed
6 years ago
3
Different results with same phyloseq
#18
sfeds
closed
6 years ago
2
How low is my "low biomass"?
#17
sarasary82
closed
6 years ago
1
Error with isContaminant
#16
EAFrench
closed
6 years ago
1
Prevalence filtering after decontam?
#15
sachasuca
closed
6 years ago
1
Issue running prevalence method with isContaminant
#14
nmshahir
closed
6 years ago
6
Identify contaminants by frequency - errors and warnings in r
#13
stangedal
closed
6 years ago
8
Missing data and different measures of concentration
#12
stangedal
closed
6 years ago
2
How to get the taxa names of contaminants
#11
kbcn
closed
6 years ago
3
Removing taxa on a per batch basis
#10
LewisNU
closed
6 years ago
1
Individual blanks/control samples
#9
st01565
closed
6 years ago
4
Sample Data
#8
ghost
closed
6 years ago
2
isContaminant produces all NaN, due to zero-read sample
#7
roey-angel
closed
6 years ago
6
Edge cases (undetectable quant, low biomass)
#6
fanli-gcb
opened
7 years ago
2
Documentation for preparing or cleaning input data
#5
lakarstens
closed
7 years ago
1
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