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customProDB
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0
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1
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657
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
17 months ago
Esraa
• 0
0
votes
1
reply
645
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 18 months ago by
James W. MacDonald
67k • written 18 months ago by
Esraa
• 0
0
votes
0
replies
396
views
customProDB: error aberrant fasta from SNV
customProDB
21 months ago
finoa.li
• 0
0
votes
0
replies
591
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
2.3 years ago
04.marshal-decibel
• 0
0
votes
0
replies
956
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
2.3 years ago
04.marshal-decibel
• 0
0
votes
1
reply
889
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
5.0 years ago
laura.fancello
• 0
0
votes
1
reply
1000
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
5.3 years ago
Elena.M
• 0
4
votes
9
replies
3.6k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 5 months ago by
Yun
• 0 • written 5.7 years ago by
daniel.magnus.bader
▴ 50
0
votes
1
reply
1.1k
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 6.2 years ago by
xiaojing.wang
▴ 50 • written 6.2 years ago by
iranmdl15
• 0
0
votes
1
reply
1.1k
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 6.3 years ago by
xiaojing.wang
▴ 50 • written 6.4 years ago by
samupatt
• 0
0
votes
1
reply
1.1k
views
aaVariation function bug (Methonine instead of Leucine)
customprodb
translation
updated 6.3 years ago by
xiaojing.wang
▴ 50 • written 6.6 years ago by
georges.bedran
• 0
0
votes
3
replies
1.9k
views
calculateRPKM error in customProDB
software error
customprodb
updated 2.9 years ago by
Anne
• 0 • written 7.3 years ago by
javamng
▴ 10
0
votes
0
replies
1.1k
views
Annotation package generation error for customprodb for hg38
customprodb
6.8 years ago
arunima2
• 0
1
vote
1
reply
1.6k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 2.9 years ago by
Anne
• 0 • written 7.3 years ago by
javamng
▴ 10
0
votes
1
reply
1.2k
views
customProDB, OutputVarproseq function update (snvproseq)
customprodb
updated 7.9 years ago by
xiaojing.wang
▴ 50 • written 7.9 years ago by
georges.bedran
• 0
0
votes
0
replies
1.3k
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
8.2 years ago
yeh234
• 0
0
votes
1
reply
1.2k
views
CustomproDB JunctionType function
customprodb
updated 8.4 years ago by
xiaojing.wang
▴ 50 • written 8.4 years ago by
georges.bedran
• 0
0
votes
1
reply
1.2k
views
Pull request for customProDB package
customProDB
featurerequest
updated 8.5 years ago by
Dan Tenenbaum
★ 8.2k • written 8.5 years ago by
matt.chambers42
▴ 10
2
votes
4
replies
2.1k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 9.3 years ago by
xiaojing.wang
▴ 50 • written 9.3 years ago by
kristenbeck527
• 0
2
votes
2
replies
1.8k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 9.3 years ago by
xiaojing.wang
▴ 50 • written 9.3 years ago by
kristenbeck527
• 0
2
votes
4
replies
1.9k
views
customProDB: issues getting dbSNP data for non-model organism
ensembl
macaque
dbsnp
customprodb
updated 9.3 years ago by
xiaojing.wang
▴ 50 • written 9.3 years ago by
kristenbeck527
• 0
21 results • Page
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Recent ...
Replies
Comment: Differential Expression Analysis with unbalanced batches without replication bet
by
Thili
• 0
Thank you for your reply. I currently have batch-corrected data processed with scvi-tools (specifically, totalvi) and have followed the sam…
Comment: Problem at champ.load
by
andrew.gibbons
• 0
I'd love to know if anyone has a workaround too. I've tried rolling back ChAMP and R to the previous versions that others have said work wi…
Comment: GOstats kegg analysis in wheat - help - none of the objects in the first column
by
GV Yoshikawa
• 0
Thank you for the reply. I tried swapping columns before asking, it made no difference. head(keggframeData) path_id kegg…
Answer: Differential Expression Analysis with unbalanced batches without replication bet
by
Gordon Smyth
51k
> Is there an alternative model or approach in tools like edgeR, limma-voom, or DESeq2 or any other that can handle confounded batch effect…
Comment: BiomaRt Possible Ensembl SSL connectivity problems detected.
by
Adam
• 0
I just found this workaround: httr::set_config(config(ssl_verifypeer = FALSE, ssl_verifyhost = FALSE)) at [this Stack Overflow link][…
Votes
A: Up/Down Regulated GeneList from edgeR and R
A: Up/Down Regulated GeneList from edgeR and R
A: Down/Up-regulated genes asymmetry in edgeR differential expression analysis
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
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