Showing : DECIPHER • reset
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Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
20 days ago Maggie • 0
1
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3
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909
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Non-zero exit status error when installing GenomeInfoDbData
DECIPHER GenomeInfoDbData Bioconductor GenomeInfoDb
written 5 months ago by • 0
0
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2
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449
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DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
8 months ago makala • 0
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0
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528
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LearnTaxa with custom Silva
DECIPHER LearnTaxa
9 months ago Eryn • 0
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2
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1.2k
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convert sequences disambiguated with DECIPHER back to FASTA
DECIPHER FASTA disambiguate
written 4.7 years ago by • 0
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3
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1.2k
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DECIPHER IdTaxa: Speed up training?
DECIPHER idtaxa
updated 19 months ago by ▴ 150 • written 19 months ago by ▴ 30
3
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5
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2.3k
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Error: 'IdClusters'
DECIPHER
updated 20 months ago by ▴ 10 • written 23 months ago by • 0
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543
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Updating 16S training set with LearnTaxa
DECIPHER
2.1 years ago Connor • 0
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3
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1.4k
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Problem with multiple sequence alignment using AlignSeqs
R dada2 DECIPHER
updated 2.1 years ago by ▴ 150 • written 2.2 years ago by • 0
0
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1
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980
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OligoArrayAux fails to compile
DECIPHER
2.2 years ago fabian.roger08 ▴ 10
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3
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1.6k
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Issue::DesignPrimers DECIPHER
DECIPHER DesignPrimers
updated 3.4 years ago by • 0 • written 3.4 years ago by • 0
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1
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972
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ORF finding in DECIPHER
ORF DECIPHER ORFhunteR
updated 3.6 years ago by ▴ 150 • written 3.6 years ago by • 0
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5
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2.7k
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Do DECIPHER:IdTaxa / dada2::assignTaxonomy work with ambigious reference training set?
decipher dada2
updated 3.7 years ago by ▴ 10 • written 5.0 years ago by • 0
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5
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1.9k
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DECIPHER maximum allowable size
DECIPHER Alignment alig
updated 3.7 years ago by ▴ 150 • written 3.7 years ago by ▴ 10
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1.2k
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DECIPHER Package on dada2 -Implementing Silva_metaxa2 training set from qza file into a fastq.gz/.Rdata
DECIPHER dada2
3.8 years ago anrongloh • 0
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1
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1.1k
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Defining groups in Decipher by sequence position in the database (FASTA)
DefiningGroups RStudio DECIPHER Specificprimers
updated 3.9 years ago by ▴ 150 • written 3.9 years ago by • 0
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5
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2.1k
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Program not properly installed/program not accessible by system
R decipher
updated 3.9 years ago by ▴ 150 • written 4.8 years ago by • 0
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0
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1.0k
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DECIPHER Probe Design Questions
DECIPHER
4.2 years ago henry1995910343 • 0
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2
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1.0k
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insufficient alignment
DECIPHER Alignment
4.2 years ago julius_vn • 0
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3
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2.1k
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DECIPHER save alignement in outputs
msa decipher output prettyPrint
updated 4.4 years ago by ▴ 300 • written 4.4 years ago by • 0
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6
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2.3k
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Issue with DECIPHER::IdTaxa
DECIPHER IdTaxa
4.4 years ago sebastian.mynott • 0
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2
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1.2k
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how to design probes using decipher
R decipher
4.7 years ago hoonhuiyi • 0
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5
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4.5k
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Error in (function (classes, fdef, mtable)
software error DECIPHER
updated 4.8 years ago by 4.1k • written 4.8 years ago by • 0
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21
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3.6k
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How to use DECIPHER to design group-specific primers
Decipher
4.8 years ago hoonhuiyi • 0
0
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1
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1.2k
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DECIPHER::AlignSeqs fails with a large guide tree
DECIPHER
updated 5.0 years ago by ▴ 150 • written 5.0 years ago by ▴ 10
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1
reply
929
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PCR simulation with PNAs
PCR DECIPHER PNA
5.3 years ago marissaruthlee • 0
1
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2
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1.7k
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Display BrowseSeqs output in R Notebook?
BrowseSeqs DECIPHER notebook rmarkdown
updated 5.4 years ago by ▴ 150 • written 5.4 years ago by • 0
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0
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891
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Alignment larger than the maximum allowable size
DECIPHER
updated 5.6 years ago by 4.1k • written 5.6 years ago by • 0
2
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4
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2.2k
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How to get sequence homology percent from a multiple sequence alignment in DECIPHER?
decipher r protein alignment
6.8 years ago reubenmcgregor88 • 0
2
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2
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2.4k
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How to combine sequences from different stringsets?
biostrings decipher
updated 7.0 years ago by ★ 6.6k • written 7.0 years ago by • 0
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3
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1.5k
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Transform index to chromosome in DECIPHER package
decipher
updated 7.1 years ago by ▴ 150 • written 7.1 years ago by ▴ 40
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7
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2.0k
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Is it possible to do an alignment to a chosen reference sequence in DECIPHER?
R decipher biostrings
updated 7.1 years ago by ▴ 150 • written 7.1 years ago by • 0
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2
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1.2k
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Is it possible to import many .tsr sequence file into R using bio strings for use in DECIPHER?
r biostrings decipher
7.1 years ago reubenmcgregor88 • 0
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5
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2.0k
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Colour a phylogenetic tree, based on column in DECIPHER?
r decipher biostrings
updated 7.1 years ago by ▴ 150 • written 7.1 years ago by • 0
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3
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2.1k
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Is it possible to import a multiple fasta alignemnt (.mfa) file into DECIPHER?
decipher DNA biostrings
updated 7.1 years ago by ▴ 150 • written 7.1 years ago by • 0
0
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1
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1.4k
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DECIPHER - AlignSeqs error is.leaf(dend) node stack overflow
decipher alignment
updated 7.3 years ago by ▴ 10 • written 7.3 years ago by • 0
0
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1
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1.8k
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AlignSeqs error: protect(): protection stack overflow
multiplealignment decipher
7.3 years ago c.l.frankling • 0
2
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5
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2.2k
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Multiple Sequence Alignment using DNA sequence
msa decipher
7.7 years ago bbista91 ▴ 10
1
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5
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1.8k
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DECIPHER version bug using biocLite()
DECIPHER
8.6 years ago Vinicius Henrique da Silva ▴ 40
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1
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1.1k
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Possible bug in ConsensusSequence
DECIPHER
updated 8.7 years ago by ▴ 10 • written 8.7 years ago by • 0
0
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3
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3.0k
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mt.teststat
multtest DECIPHER multtest DECIPHER
updated 9.0 years ago by ▴ 20 • written 21.8 years ago by ▴ 220
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1.7k
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Job: Bioinformatics Postdoc Position at the IMB, Mainz
Genetics DECIPHER Genetics DECIPHER
10.9 years ago Kathi Zarnack ▴ 110
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1
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1.3k
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Agi4x44PreProcess: Replicated Genes and Custom Annotation Database
Annotation zebrafish probe DECIPHER Annotation zebrafish probe DECIPHER
updated 14.5 years ago by ★ 7.2k • written 14.5 years ago by ▴ 40
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1
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2.0k
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boxplot error with expression set using oligo package and Human gene st 1.0 arrays
oligo DECIPHER oligo DECIPHER
updated 14.7 years ago by ★ 4.3k • written 14.7 years ago by ▴ 40
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0
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1.3k
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Basic Question about gcrma & exporting to excel > (command not working)
Microarray affy gcrma oligo arrayQualityMetrics DECIPHER Microarray affy gcrma oligo
14.7 years ago Dick Beyer ★ 1.4k
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1.7k
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'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
14.8 years ago Radek Blatny ▴ 60
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0
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1.8k
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Post-doc position in Paris
Sequencing Epigenetics Cancer Breast DECIPHER Sequencing Epigenetics Cancer Breast
15.6 years ago Joern Toedling ▴ 450
0
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4
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1.5k
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help with large Rgraphviz output
graph DECIPHER graph DECIPHER
updated 18.7 years ago by ★ 7.4k • written 18.7 years ago by ▴ 890
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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