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customprodb
•
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0
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1
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717
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
20 months ago
Esraa
• 0
0
votes
1
reply
726
views
Calculate RPKMs and Output proteins pass the cutoff into FASTA file ... Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse") : i…
customProDB
easyrun
error
mm10
Mus_musculus_Data
updated 21 months ago by
James W. MacDonald
68k • written 21 months ago by
Esraa
• 0
0
votes
0
replies
440
views
customProDB: error aberrant fasta from SNV
customProDB
2.1 years ago
finoa.li
• 0
0
votes
0
replies
646
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
2.5 years ago
04.marshal-decibel
• 0
0
votes
0
replies
1.0k
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
2.6 years ago
04.marshal-decibel
• 0
0
votes
1
reply
951
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
5.3 years ago
laura.fancello
• 0
0
votes
1
reply
1.1k
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
5.6 years ago
Elena.M
• 0
4
votes
9
replies
3.9k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 9 months ago by
Yun
• 0 • written 6.0 years ago by
daniel.magnus.bader
▴ 50
0
votes
1
reply
1.1k
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 6.5 years ago by
xiaojing.wang
▴ 50 • written 6.5 years ago by
iranmdl15
• 0
0
votes
1
reply
1.2k
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 6.5 years ago by
xiaojing.wang
▴ 50 • written 6.7 years ago by
samupatt
• 0
0
votes
1
reply
1.2k
views
aaVariation function bug (Methonine instead of Leucine)
customprodb
translation
updated 6.5 years ago by
xiaojing.wang
▴ 50 • written 6.9 years ago by
georges.bedran
• 0
0
votes
3
replies
1.9k
views
calculateRPKM error in customProDB
software error
customprodb
updated 3.2 years ago by
Anne
• 0 • written 7.6 years ago by
javamng
▴ 10
0
votes
0
replies
1.1k
views
Annotation package generation error for customprodb for hg38
customprodb
7.0 years ago
arunima2
• 0
1
vote
1
reply
1.6k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 3.2 years ago by
Anne
• 0 • written 7.6 years ago by
javamng
▴ 10
0
votes
1
reply
1.2k
views
customProDB, OutputVarproseq function update (snvproseq)
customprodb
updated 8.2 years ago by
xiaojing.wang
▴ 50 • written 8.2 years ago by
georges.bedran
• 0
0
votes
0
replies
1.3k
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
8.5 years ago
yeh234
• 0
0
votes
1
reply
1.3k
views
CustomproDB JunctionType function
customprodb
updated 8.7 years ago by
xiaojing.wang
▴ 50 • written 8.7 years ago by
georges.bedran
• 0
0
votes
1
reply
1.3k
views
Pull request for customProDB package
customProDB
featurerequest
updated 8.8 years ago by
Dan Tenenbaum
★ 8.2k • written 8.8 years ago by
matt.chambers42
▴ 10
2
votes
4
replies
2.1k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 9.6 years ago by
xiaojing.wang
▴ 50 • written 9.6 years ago by
kristenbeck527
• 0
2
votes
2
replies
1.9k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 9.6 years ago by
xiaojing.wang
▴ 50 • written 9.6 years ago by
kristenbeck527
• 0
2
votes
4
replies
2.0k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl
macaque
dbsnp
customprodb
updated 9.6 years ago by
xiaojing.wang
▴ 50 • written 9.6 years ago by
kristenbeck527
• 0
21 results • Page
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Answer: WGCNA with paired samples
by
Ivo
• 0
You can use batch correction on the person ID and then continue WGCNA as usual using the corrected matrix. You can use e.g. sva::ComBat or …
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The function uses ggplot2, so you need `+ ggtitle('title')`. Please take a ggplot2 tutorial for details.
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I apologize, but I am still perplexed. I need to know the exact type of replication. Do we have many samples taken from the same tumor? You…
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VST is valid for working with expression data on a variance stabilized scale, so yes. There are many papers that have used VST and then com…
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52k
It is usual to analyse log normalized values from Olink in limma. Just a straight log transformation should be sufficient. We find that `tr…
Votes
Comment: Different annotation packages (org.Mm.eg.db, EnsDb.Mmusculus.v79, BiomaRt) retu
Answer: normalizatino of dna methylation EPIC data
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
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