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customProDB
•
reset
0
votes
0
replies
38
views
customProDB: error aberrant fasta from SNV
customProDB
8 days ago
finoa.li
• 0
0
votes
0
replies
132
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
6 months ago
04.marshal-decibel
• 0
0
votes
0
replies
196
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
7 months ago
04.marshal-decibel
• 0
0
votes
3
replies
1.3k
views
calculateRPKM error in customProDB
software error
customprodb
updated 14 months ago by
Anne
• 0 • written 5.5 years ago by
javamng
▴ 10
1
vote
1
reply
1.1k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 14 months ago by
Anne
• 0 • written 5.5 years ago by
javamng
▴ 10
0
votes
1
reply
472
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
3.3 years ago
laura.fancello
• 0
0
votes
1
reply
420
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
3.6 years ago
Elena.M
• 0
3
votes
8
replies
1.7k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
3.9 years ago
daniel.magnus.bader
▴ 40
0
votes
1
reply
576
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 4.4 years ago by
xiaojing.wang
▴ 50 • written 4.4 years ago by
iranmdl15
• 0
0
votes
1
reply
569
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 4.5 years ago by
xiaojing.wang
▴ 50 • written 4.6 years ago by
samupatt
• 0
0
votes
1
reply
606
views
aaVariation function bug (Methonine instead of Leucine)
customprodb
translation
updated 4.5 years ago by
xiaojing.wang
▴ 50 • written 4.8 years ago by
georges.bedran
• 0
0
votes
0
replies
623
views
Annotation package generation error for customprodb for hg38
customprodb
5.0 years ago
arunima2
• 0
0
votes
1
reply
788
views
customProDB, OutputVarproseq function update (snvproseq)
customprodb
updated 6.1 years ago by
xiaojing.wang
▴ 50 • written 6.2 years ago by
georges.bedran
• 0
0
votes
0
replies
847
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
6.5 years ago
yeh234
• 0
0
votes
1
reply
762
views
CustomproDB JunctionType function
customprodb
updated 6.6 years ago by
xiaojing.wang
▴ 50 • written 6.6 years ago by
georges.bedran
• 0
0
votes
1
reply
776
views
Pull request for customProDB package
customProDB
featurerequest
updated 6.7 years ago by
Dan Tenenbaum
★ 8.2k • written 6.7 years ago by
matt.chambers42
▴ 10
2
votes
4
replies
1.3k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 7.6 years ago by
xiaojing.wang
▴ 50 • written 7.6 years ago by
kristenbeck527
• 0
2
votes
2
replies
1.2k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 7.6 years ago by
xiaojing.wang
▴ 50 • written 7.6 years ago by
kristenbeck527
• 0
2
votes
4
replies
1.2k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl
macaque
dbsnp
customprodb
updated 7.6 years ago by
xiaojing.wang
▴ 50 • written 7.6 years ago by
kristenbeck527
• 0
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Comment: Which input file is used for DGEList in EgdeR?
by
mohammedtoufiq91
▴ 10
Thank you @gordonsmyth My collaborator asked me to test this pipeline with `egdeR` package. We are interested at gene level analysis only…
Answer: Why in Bioconductor community people rarely upvote questions?
by
Gordon Smyth
47k
I think it is a good idea to start a discussion with correct information. Looking back through Bioconductor Support records, it is not at a…
Comment: How to identify top most variable genes from log2 normalized data?
by
Gordon Smyth
47k
Your code doesn't look right to me. I think you're using order() where sort() would be more appropriate. To order your cpm matrix by row v…
Comment: How to load fasta file with openPrimeR?
by
Santiago Edilberto
• 0
> library(openPrimeR) There are missing/non-functioning external tools. To use the full potential of openPrimeR, please mak…
Answer: Which input file is used for DGEList in EgdeR?
by
Gordon Smyth
47k
I use and recommend featureCounts. Despite all that has been written on this topic, I still think that direct gene counting is faster and m…
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Answer: Which input file is used for DGEList in EgdeR?
Answer: Identifying DEGs using lfcshrink()
Answer: Is this DESeq2 interactions design correct?
Comment: STRINGdb string_db$map error
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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