Showing : decipher • reset
1
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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
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3
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370
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DECIPHER DesignProbes unable to design FISH-probes
decipher FISH DECIPHER FISH-probe probe-design
written 11 weeks ago by • 0
0
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2
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530
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Memory error while running alignments
DECIPHER Alignment
updated 12 weeks ago by ★ 4.0k • written 6 months ago by • 0
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2
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1.1k
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Issue when attempting to use output from DECIPHER IDtaxa (pr2 V5) with dada2/phyloseq
DECIPHER taxonomyassignment phyloseq dada2 Pr2V5
updated 11 months ago by • 0 • written 13 months ago by • 0
1
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3
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1.8k
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Non-zero exit status error when installing GenomeInfoDbData
DECIPHER GenomeInfoDbData Bioconductor GenomeInfoDb
written 17 months ago by • 0
0
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2
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902
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DECIPHER::idTaxa - broken link to download GTDB r220 (modified) trainig set
DECIPHER
21 months ago makala • 0
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0
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1.1k
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LearnTaxa with custom Silva
DECIPHER LearnTaxa
22 months ago Eryn • 0
0
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2
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1.5k
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convert sequences disambiguated with DECIPHER back to FASTA
DECIPHER FASTA disambiguate
written 5.7 years ago by • 0
0
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3
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1.8k
views
DECIPHER IdTaxa: Speed up training?
DECIPHER idtaxa
updated 2.6 years ago by ▴ 160 • written 2.6 years ago by ▴ 30
3
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5
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3.1k
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Error: 'IdClusters'
DECIPHER
updated 2.7 years ago by ▴ 10 • written 3.0 years ago by • 0
0
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0
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838
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Updating 16S training set with LearnTaxa
DECIPHER
3.2 years ago Connor • 0
0
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3
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1.9k
views
Problem with multiple sequence alignment using AlignSeqs
R dada2 DECIPHER
updated 3.2 years ago by ▴ 160 • written 3.2 years ago by • 0
0
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1
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1.5k
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OligoArrayAux fails to compile
DECIPHER
3.3 years ago • updated 3.2 years ago fabian.roger08 ▴ 10
0
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3
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2.1k
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Issue::DesignPrimers DECIPHER
DECIPHER DesignPrimers
updated 4.4 years ago by • 0 • written 4.4 years ago by • 0
0
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1
reply
1.2k
views
ORF finding in DECIPHER
ORF DECIPHER ORFhunteR
updated 4.7 years ago by ▴ 160 • written 4.7 years ago by • 0
0
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5
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3.7k
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Do DECIPHER:IdTaxa / dada2::assignTaxonomy work with ambigious reference training set?
decipher dada2
updated 4.7 years ago by ▴ 10 • written 6.0 years ago by • 0
0
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5
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2.4k
views
DECIPHER maximum allowable size
DECIPHER Alignment alig
updated 4.7 years ago by ▴ 160 • written 4.8 years ago by ▴ 10
0
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0
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1.7k
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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
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1
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1.4k
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Defining groups in Decipher by sequence position in the database (FASTA)
DefiningGroups RStudio DECIPHER Specificprimers
updated 5.0 years ago by ▴ 160 • written 5.0 years ago by • 0
0
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5
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2.6k
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Program not properly installed/program not accessible by system
R decipher
updated 4.9 years ago by ▴ 160 • written 5.8 years ago by • 0
0
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0
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1.4k
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DECIPHER Probe Design Questions
DECIPHER
5.2 years ago henry1995910343 • 0
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2
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1.3k
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insufficient alignment
DECIPHER Alignment
5.3 years ago julius_vn • 0
0
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3
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2.8k
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DECIPHER save alignement in outputs
msa decipher output prettyPrint
updated 5.4 years ago by ▴ 300 • written 5.4 years ago by • 0
1
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7
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3.2k
views
Issue with DECIPHER::IdTaxa
DECIPHER IdTaxa
updated 11 months ago by • 0 • written 5.5 years ago by • 0
0
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2
replies
1.5k
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how to design probes using decipher
R decipher
5.8 years ago hoonhuiyi • 0
0
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5
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5.0k
views
Error in (function (classes, fdef, mtable)
software error DECIPHER
updated 5.8 years ago by 4.3k • written 5.8 years ago by • 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
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1
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1.4k
views
DECIPHER::AlignSeqs fails with a large guide tree
DECIPHER
updated 6.1 years ago by ▴ 160 • written 6.1 years ago by ▴ 10
0
votes
1
reply
1.3k
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PCR simulation with PNAs
PCR DECIPHER PNA
6.4 years ago marissaruthlee • 0
1
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2
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2.2k
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Display BrowseSeqs output in R Notebook?
BrowseSeqs DECIPHER notebook rmarkdown
updated 6.4 years ago by ▴ 160 • written 6.4 years ago by • 0
0
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0
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1.1k
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Alignment larger than the maximum allowable size
DECIPHER
updated 6.6 years ago by 4.3k • written 6.6 years ago by • 0
2
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4
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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
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2
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2.9k
views
How to combine sequences from different stringsets?
biostrings decipher
updated 8.0 years ago by ★ 6.6k • written 8.0 years ago by • 0
1
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3
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1.8k
views
Transform index to chromosome in DECIPHER package
decipher
updated 8.1 years ago by ▴ 160 • written 8.1 years ago by ▴ 40
5
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7
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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 ▴ 160 • written 8.1 years ago by • 0
0
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2
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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
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5
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2.6k
views
Colour a phylogenetic tree, based on column in DECIPHER?
r decipher biostrings
updated 8.1 years ago by ▴ 160 • written 8.1 years ago by • 0
2
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3
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2.6k
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Is it possible to import a multiple fasta alignemnt (.mfa) file into DECIPHER?
decipher DNA biostrings
updated 8.2 years ago by ▴ 160 • written 8.2 years ago by • 0
0
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1
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1.7k
views
DECIPHER - AlignSeqs error is.leaf(dend) node stack overflow
decipher alignment
updated 8.3 years ago by ▴ 10 • written 8.3 years ago by • 0
0
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1
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2.2k
views
AlignSeqs error: protect(): protection stack overflow
multiplealignment decipher
8.4 years ago c.l.frankling • 0
2
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5
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2.7k
views
Multiple Sequence Alignment using DNA sequence
msa decipher
8.7 years ago bbista91 ▴ 10
1
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5
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2.3k
views
DECIPHER version bug using biocLite()
DECIPHER
9.7 years ago Vinicius Henrique da Silva ▴ 40
0
votes
1
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1.3k
views
Possible bug in ConsensusSequence
DECIPHER
updated 9.8 years ago by ▴ 10 • written 9.8 years ago by • 0
0
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3
replies
3.3k
views
mt.teststat
multtest DECIPHER multtest DECIPHER
updated 10.1 years ago by ▴ 20 • written 22.9 years ago by ▴ 220
0
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0
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2.0k
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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 ★ 7.2k • written 15.5 years ago by ▴ 40
0
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1
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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 ★ 4.3k • written 15.7 years ago by ▴ 40
0
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0
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1.5k
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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
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0
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2.0k
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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
15.9 years ago Radek Blatny ▴ 60
0
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0
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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 1 of 2
Recent ...
Replies
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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