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customProDB
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0
votes
1
reply
872
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
2.4 years ago
Esraa
• 0
0
votes
1
reply
889
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 2.5 years ago by
James W. MacDonald
68k • written 2.5 years ago by
Esraa
• 0
0
votes
0
replies
543
views
customProDB: error aberrant fasta from SNV
customProDB
2.8 years ago
finoa.li
• 0
0
votes
0
replies
787
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
3.3 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
3.3 years ago
04.marshal-decibel
• 0
0
votes
1
reply
1.1k
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
6.0 years ago
laura.fancello
• 0
0
votes
1
reply
1.3k
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
6.3 years ago
Elena.M
• 0
4
votes
9
replies
4.5k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 18 months ago by
Yun
• 0 • written 6.7 years ago by
daniel.magnus.bader
▴ 50
0
votes
1
reply
1.3k
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 7.2 years ago by
xiaojing.wang
▴ 50 • written 7.2 years ago by
iranmdl15
• 0
0
votes
1
reply
1.3k
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 7.3 years ago by
xiaojing.wang
▴ 50 • written 7.4 years ago by
samupatt
• 0
0
votes
1
reply
1.3k
views
aaVariation function bug (Methonine instead of Leucine)
customprodb
translation
updated 7.3 years ago by
xiaojing.wang
▴ 50 • written 7.6 years ago by
georges.bedran
• 0
0
votes
3
replies
2.2k
views
calculateRPKM error in customProDB
software error
customprodb
updated 3.9 years ago by
Anne
• 0 • written 8.3 years ago by
javamng
▴ 10
0
votes
0
replies
1.2k
views
Annotation package generation error for customprodb for hg38
customprodb
7.8 years ago
arunima2
• 0
1
vote
1
reply
1.8k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 3.9 years ago by
Anne
• 0 • written 8.3 years ago by
javamng
▴ 10
0
votes
1
reply
1.3k
views
customProDB, OutputVarproseq function update (snvproseq)
customprodb
updated 8.9 years ago by
xiaojing.wang
▴ 50 • written 8.9 years ago by
georges.bedran
• 0
0
votes
0
replies
1.4k
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
9.2 years ago
yeh234
• 0
0
votes
1
reply
1.4k
views
CustomproDB JunctionType function
customprodb
updated 9.4 years ago by
xiaojing.wang
▴ 50 • written 9.4 years ago by
georges.bedran
• 0
0
votes
1
reply
1.4k
views
Pull request for customProDB package
customProDB
featurerequest
updated 9.5 years ago by
Dan Tenenbaum
★ 8.2k • written 9.5 years ago by
matt.chambers42
▴ 10
2
votes
4
replies
2.4k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 10.3 years ago by
xiaojing.wang
▴ 50 • written 10.3 years ago by
kristenbeck527
• 0
2
votes
2
replies
2.1k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 10.3 years ago by
xiaojing.wang
▴ 50 • written 10.3 years ago by
kristenbeck527
• 0
2
votes
4
replies
2.2k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl
macaque
dbsnp
customprodb
updated 10.3 years ago by
xiaojing.wang
▴ 50 • written 10.3 years ago by
kristenbeck527
• 0
21 results • Page
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Recent ...
Replies
Answer: After running samtools, the featureCounts command crashed.
by
Kevin Blighe
★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot
by
Kevin Blighe
★ 4.0k
Hi bioinffun, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to …
Answer: gene Set with high AUC score but no cells assigned to cell type
by
Kevin Blighe
★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction
by
Kevin Blighe
★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Answer: Streamlining the computing time for MiloDE p-value correction in large dataset?
by
Kevin Blighe
★ 4.0k
Hi Joseph, I agree with ATpoint's suggestion that pseudobulk aggregation (e.g., via aggregateData in scran or similar) would likely be f…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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