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customProDB
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487
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
11 months ago
Esraa
• 0
0
votes
1
reply
501
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 12 months ago by
James W. MacDonald
66k • written 12 months ago by
Esraa
• 0
0
votes
0
replies
301
views
customProDB: error aberrant fasta from SNV
customProDB
16 months ago
finoa.li
• 0
0
votes
0
replies
469
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
22 months ago
04.marshal-decibel
• 0
0
votes
0
replies
818
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
23 months ago
04.marshal-decibel
• 0
0
votes
1
reply
772
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
4.6 years ago
laura.fancello
• 0
0
votes
1
reply
832
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
4.9 years ago
Elena.M
• 0
4
votes
9
replies
3.2k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 16 days ago by
Yun
• 0 • written 5.2 years ago by
daniel.magnus.bader
▴ 50
0
votes
1
reply
945
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 5.7 years ago by
xiaojing.wang
▴ 50 • written 5.7 years ago by
iranmdl15
• 0
0
votes
1
reply
931
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 5.8 years ago by
xiaojing.wang
▴ 50 • written 5.9 years ago by
samupatt
• 0
0
votes
1
reply
956
views
aaVariation function bug (Methonine instead of Leucine)
customprodb
translation
updated 5.8 years ago by
xiaojing.wang
▴ 50 • written 6.1 years ago by
georges.bedran
• 0
0
votes
3
replies
1.7k
views
calculateRPKM error in customProDB
software error
customprodb
updated 2.5 years ago by
Anne
• 0 • written 6.8 years ago by
javamng
▴ 10
0
votes
0
replies
933
views
Annotation package generation error for customprodb for hg38
customprodb
6.3 years ago
arunima2
• 0
1
vote
1
reply
1.5k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 2.5 years ago by
Anne
• 0 • written 6.8 years ago by
javamng
▴ 10
0
votes
1
reply
1.1k
views
customProDB, OutputVarproseq function update (snvproseq)
customprodb
updated 7.5 years ago by
xiaojing.wang
▴ 50 • written 7.5 years ago by
georges.bedran
• 0
0
votes
0
replies
1.1k
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
7.8 years ago
yeh234
• 0
0
votes
1
reply
1.1k
views
CustomproDB JunctionType function
customprodb
updated 7.9 years ago by
xiaojing.wang
▴ 50 • written 7.9 years ago by
georges.bedran
• 0
0
votes
1
reply
1.1k
views
Pull request for customProDB package
customProDB
featurerequest
updated 8.0 years ago by
Dan Tenenbaum
★ 8.2k • written 8.0 years ago by
matt.chambers42
▴ 10
2
votes
4
replies
1.9k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 8.9 years ago by
xiaojing.wang
▴ 50 • written 8.9 years ago by
kristenbeck527
• 0
2
votes
2
replies
1.7k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 8.9 years ago by
xiaojing.wang
▴ 50 • written 8.9 years ago by
kristenbeck527
• 0
2
votes
4
replies
1.7k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl
macaque
dbsnp
customprodb
updated 8.9 years ago by
xiaojing.wang
▴ 50 • written 8.9 years ago by
kristenbeck527
• 0
21 results • Page
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Recent ...
Replies
Comment: How to compare subset of samples from VCF files
by
Gordon Smyth
50k
Welcome to Bioconductor support. Did you know that you can delete your old postings if they haven't received an answer yet? Instead of ap…
Comment: How to compare subset of samples from VCF files
by
Marco
• 0
Here's the vcf file as code block ``` ##fileformat=VCFv4.2 ##INFO=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth"> ##FOR…
Comment: Gviz and custom database
by
James W. MacDonald
66k
The vignette for `Gviz` says you can use a `DNAStringSet`, generated using `Biostrings`. Have you tried that?
Comment: Gviz and custom database
by
luigi.faino
• 0
Dear, this is not what I need. I need to transform a fasta sequence in a genome track usable in Gviz. L
Answer: Gviz and custom database
by
James W. MacDonald
66k
https://bioconductor.org/packages/release/bioc/vignettes/txdbmaker/inst/doc/txdbmaker.html
Votes
Answer: makeExampleDESeqDataSet using pilot data
Answer: Checking/updating package versions
Answer: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)?
convert data frame of Entrez IDs to Gene Symbols
Answer: LRT, pairwise comparisons and p-value adjustment
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Fred Hutch (Recruiting)
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James W. MacDonald
66k
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Levi Waldron
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