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decipher
•
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1
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2
replies
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Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy names?
silva
decipher
DECIPHER
1 day ago • updated 23 hours ago
Korneel
• 0
0
votes
3
replies
370
views
DECIPHER DesignProbes unable to design FISH-probes
decipher
FISH
DECIPHER
FISH-probe
probe-design
written 11 weeks ago by
vreinmuth
• 0
0
votes
2
replies
530
views
Memory error while running alignments
DECIPHER
Alignment
updated 12 weeks ago by
Kevin Blighe
★ 4.0k • written 6 months ago by
Mihir
• 0
0
votes
2
replies
1.1k
views
Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER
taxonomyassignment
phyloseq
dada2
Pr2V5
updated 11 months ago by
Daniel
• 0 • written 13 months ago by
Maggie
• 0
1
vote
3
replies
1.8k
views
Non-zero exit status error when installing GenomeInfoDbData
DECIPHER
GenomeInfoDbData
Bioconductor
GenomeInfoDb
written 17 months ago by
dbjohnson7
• 0
0
votes
2
replies
902
views
DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
21 months ago
makala
• 0
0
votes
0
replies
1.1k
views
LearnTaxa with custom Silva
DECIPHER
LearnTaxa
22 months ago
Eryn
• 0
0
votes
2
replies
1.5k
views
convert sequences disambiguated with DECIPHER back to FASTA
DECIPHER
FASTA
disambiguate
written 5.7 years ago by
joannew
• 0
0
votes
3
replies
1.8k
views
DECIPHER IdTaxa: Speed up training?
DECIPHER
idtaxa
updated 2.6 years ago by
Erik Wright
▴ 160 • written 2.6 years ago by
Till
▴ 30
3
votes
5
replies
3.1k
views
Error: 'IdClusters'
DECIPHER
updated 2.7 years ago by
Ling-Hsiu
▴ 10 • written 3.0 years ago by
julieta.micorriza
• 0
0
votes
0
replies
838
views
Updating 16S training set with LearnTaxa
DECIPHER
3.2 years ago
Connor
• 0
0
votes
3
replies
1.9k
views
Problem with multiple sequence alignment using AlignSeqs
R
dada2
DECIPHER
updated 3.2 years ago by
Erik Wright
▴ 160 • written 3.2 years ago by
Nelli
• 0
0
votes
1
reply
1.5k
views
OligoArrayAux fails to compile
DECIPHER
3.3 years ago • updated 3.2 years ago
fabian.roger08
▴ 10
0
votes
3
replies
2.1k
views
Issue::DesignPrimers DECIPHER
DECIPHER
DesignPrimers
updated 4.4 years ago by
slwmartin
• 0 • written 4.4 years ago by
Mailys
• 0
0
votes
1
reply
1.2k
views
ORF finding in DECIPHER
ORF
DECIPHER
ORFhunteR
updated 4.7 years ago by
Erik Wright
▴ 160 • written 4.7 years ago by
tkirkland
• 0
0
votes
5
replies
3.7k
views
Do DECIPHER:IdTaxa / dada2::assignTaxonomy work with ambigious reference training set?
decipher
dada2
updated 4.7 years ago by
fabian.roger08
▴ 10 • written 6.0 years ago by
fabian.roger
• 0
0
votes
5
replies
2.4k
views
DECIPHER maximum allowable size
DECIPHER
Alignment
alig
updated 4.7 years ago by
Erik Wright
▴ 160 • written 4.8 years ago by
curiousmind007
▴ 10
0
votes
0
replies
1.7k
views
DECIPHER Package on dada2 -Implementing Silva_metaxa2 training set from qza file into a fastq.gz/.Rdata
DECIPHER
dada2
4.9 years ago
anrongloh
• 0
0
votes
1
reply
1.4k
views
Defining groups in Decipher by sequence position in the database (FASTA)
DefiningGroups
RStudio
DECIPHER
Specificprimers
updated 5.0 years ago by
Erik Wright
▴ 160 • written 5.0 years ago by
noeliaruizalonso23
• 0
0
votes
5
replies
2.6k
views
Program not properly installed/program not accessible by system
R
decipher
updated 4.9 years ago by
Erik Wright
▴ 160 • written 5.8 years ago by
hoonhuiyi
• 0
0
votes
0
replies
1.4k
views
DECIPHER Probe Design Questions
DECIPHER
5.2 years ago
henry1995910343
• 0
0
votes
2
replies
1.3k
views
insufficient alignment
DECIPHER
Alignment
5.3 years ago
julius_vn
• 0
0
votes
3
replies
2.8k
views
DECIPHER save alignement in outputs
msa
decipher
output
prettyPrint
updated 5.4 years ago by
UBod
▴ 300 • written 5.4 years ago by
matamunee
• 0
1
vote
7
replies
3.2k
views
Issue with DECIPHER::IdTaxa
DECIPHER
IdTaxa
updated 11 months ago by
Daniel
• 0 • written 5.5 years ago by
sebastian.mynott
• 0
0
votes
2
replies
1.5k
views
how to design probes using decipher
R
decipher
5.8 years ago
hoonhuiyi
• 0
0
votes
5
replies
5.0k
views
Error in (function (classes, fdef, mtable)
software error
DECIPHER
updated 5.8 years ago by
shepherl
4.3k • written 5.8 years ago by
hoonhuiyi
• 0
0
votes
21
replies
4.8k
views
How to use DECIPHER to design group-specific primers
Decipher
5.8 years ago
hoonhuiyi
• 0
0
votes
1
reply
1.4k
views
DECIPHER::AlignSeqs fails with a large guide tree
DECIPHER
updated 6.1 years ago by
Erik Wright
▴ 160 • written 6.1 years ago by
brendan.furneaux
▴ 10
0
votes
1
reply
1.3k
views
PCR simulation with PNAs
PCR
DECIPHER
PNA
6.4 years ago
marissaruthlee
• 0
1
vote
2
replies
2.2k
views
Display BrowseSeqs output in R Notebook?
BrowseSeqs
DECIPHER
notebook
rmarkdown
updated 6.4 years ago by
Erik Wright
▴ 160 • written 6.4 years ago by
lauren.fitch
• 0
0
votes
0
replies
1.1k
views
Alignment larger than the maximum allowable size
DECIPHER
updated 6.6 years ago by
shepherl
4.3k • written 6.6 years ago by
cmasembe
• 0
2
votes
4
replies
2.6k
views
How to get sequence homology percent from a multiple sequence alignment in DECIPHER?
decipher
r
protein alignment
7.8 years ago
reubenmcgregor88
• 0
2
votes
2
replies
2.9k
views
How to combine sequences from different stringsets?
biostrings
decipher
updated 8.0 years ago by
Mike Smith
★ 6.6k • written 8.0 years ago by
reubenmcgregor88
• 0
1
vote
3
replies
1.8k
views
Transform index to chromosome in DECIPHER package
decipher
updated 8.1 years ago by
Erik Wright
▴ 160 • written 8.1 years ago by
Vinicius Henrique da Silva
▴ 40
5
votes
7
replies
2.5k
views
Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
R
decipher
biostrings
updated 8.1 years ago by
Erik Wright
▴ 160 • written 8.1 years ago by
reubenmcgregor88
• 0
0
votes
2
replies
1.6k
views
Is it possible to import many .tsr sequence file into R using bio strings for use in DECIPHER?
r
biostrings
decipher
8.1 years ago
reubenmcgregor88
• 0
2
votes
5
replies
2.6k
views
Colour a phylogenetic tree, based on column in DECIPHER?
r
decipher
biostrings
updated 8.1 years ago by
Erik Wright
▴ 160 • written 8.1 years ago by
reubenmcgregor88
• 0
2
votes
3
replies
2.6k
views
Is it possible to import a multiple fasta alignemnt (.mfa) file into DECIPHER?
decipher
DNA
biostrings
updated 8.2 years ago by
Erik Wright
▴ 160 • written 8.2 years ago by
reubenmcgregor88
• 0
0
votes
1
reply
1.7k
views
DECIPHER - AlignSeqs error is.leaf(dend) node stack overflow
decipher
alignment
updated 8.3 years ago by
Erik Wright
▴ 10 • written 8.3 years ago by
emma.berdan
• 0
0
votes
1
reply
2.2k
views
AlignSeqs error: protect(): protection stack overflow
multiplealignment
decipher
8.4 years ago
c.l.frankling
• 0
2
votes
5
replies
2.7k
views
Multiple Sequence Alignment using DNA sequence
msa
decipher
8.7 years ago
bbista91
▴ 10
1
vote
5
replies
2.3k
views
DECIPHER version bug using biocLite()
DECIPHER
9.7 years ago
Vinicius Henrique da Silva
▴ 40
0
votes
1
reply
1.3k
views
Possible bug in ConsensusSequence
DECIPHER
updated 9.8 years ago by
Erik Wright
▴ 10 • written 9.8 years ago by
rob.lanfear
• 0
0
votes
3
replies
3.3k
views
mt.teststat
multtest
DECIPHER
multtest
DECIPHER
updated 10.1 years ago by
Smeeta Shrestha
▴ 20 • written 22.9 years ago by
Park, Richard
▴ 220
0
votes
0
replies
2.0k
views
Job: Bioinformatics Postdoc Position at the IMB, Mainz
Genetics
DECIPHER
Genetics
DECIPHER
11.9 years ago
Kathi Zarnack
▴ 110
0
votes
1
reply
1.6k
views
Agi4x44PreProcess: Replicated Genes and Custom Annotation Database
Annotation
zebrafish
probe
DECIPHER
Annotation
zebrafish
probe
DECIPHER
updated 15.5 years ago by
Marc Carlson
★ 7.2k • written 15.5 years ago by
Samantha England
▴ 40
0
votes
1
reply
2.3k
views
boxplot error with expression set using oligo package and Human gene st 1.0 arrays
oligo
DECIPHER
oligo
DECIPHER
updated 15.7 years ago by
Benilton Carvalho
★ 4.3k • written 15.7 years ago by
jos matejus
▴ 40
0
votes
0
replies
1.5k
views
Basic Question about gcrma & exporting to excel > (command not working)
Microarray
affy
gcrma
oligo
arrayQualityMetrics
DECIPHER
Microarray
affy
gcrma
oligo
15.7 years ago
Dick Beyer
★ 1.4k
0
votes
0
replies
2.0k
views
'Heat Map for Genes in Dataset' in the '(project name).global.plots.pdf' output of the R-GSEA code
Genetics
Clustering
DECIPHER
Genetics
Clustering
DECIPHER
15.9 years ago
Radek Blatny
▴ 60
0
votes
0
replies
2.0k
views
Post-doc position in Paris
Sequencing
Epigenetics
Cancer
Breast
DECIPHER
Sequencing
Epigenetics
Cancer
Breast
16.6 years ago
Joern Toedling
▴ 450
51 results • Page
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Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
by
Gordon Smyth
53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa?
by
Gordon Smyth
53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name
by
Korneel
• 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics
by
yesquokkan
• 0
Hello, I was also wondering about the same issue. Did you figure it out?
Comment: [DESeq2] Changing dispersion estimates between runs of DESeq2
by
colinmccornack
• 0
FWIW: This seems to be due to architectural differences between two compute nodes I was running on, specifically with the DESeq2:::fitNbino…
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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