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customprodb
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738
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
21 months ago
Esraa
• 0
0
votes
1
reply
747
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 22 months ago by
James W. MacDonald
68k • written 22 months ago by
Esraa
• 0
0
votes
0
replies
453
views
customProDB: error aberrant fasta from SNV
customProDB
2.1 years ago
finoa.li
• 0
0
votes
0
replies
665
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
2.6 years ago
04.marshal-decibel
• 0
0
votes
0
replies
1.1k
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
2.7 years ago
04.marshal-decibel
• 0
0
votes
1
reply
973
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
5.4 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
5.7 years ago
Elena.M
• 0
4
votes
9
replies
4.0k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 10 months ago by
Yun
• 0 • written 6.1 years ago by
daniel.magnus.bader
▴ 50
0
votes
1
reply
1.2k
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 6.5 years ago by
xiaojing.wang
▴ 50 • written 6.6 years ago by
iranmdl15
• 0
0
votes
1
reply
1.2k
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 6.6 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 6.6 years ago by
xiaojing.wang
▴ 50 • written 6.9 years ago by
georges.bedran
• 0
0
votes
3
replies
2.0k
views
calculateRPKM error in customProDB
software error
customprodb
updated 3.3 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
7.1 years ago
arunima2
• 0
1
vote
1
reply
1.7k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 3.3 years ago by
Anne
• 0 • written 7.6 years ago by
javamng
▴ 10
0
votes
1
reply
1.3k
views
customProDB, OutputVarproseq function update (snvproseq)
customprodb
updated 8.3 years ago by
xiaojing.wang
▴ 50 • written 8.3 years ago by
georges.bedran
• 0
0
votes
0
replies
1.3k
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
8.6 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 8.9 years ago by
Dan Tenenbaum
★ 8.2k • written 8.9 years ago by
matt.chambers42
▴ 10
2
votes
4
replies
2.2k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 9.7 years ago by
xiaojing.wang
▴ 50 • written 9.7 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 9.7 years ago by
xiaojing.wang
▴ 50 • written 9.7 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 9.7 years ago by
xiaojing.wang
▴ 50 • written 9.7 years ago by
kristenbeck527
• 0
21 results • Page
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Recent ...
Replies
Comment: DiffBind custom normalization factor
by
Abbie
• 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2?
by
James W. MacDonald
68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore
by
Kent
• 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore
by
Michael Love
43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi
by
Michael Love
43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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