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customProDB
•
reset
3
votes
8
replies
3.0k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
5.1 years ago
daniel.magnus.bader
▴ 40
2
votes
4
replies
1.8k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 8.8 years ago by
xiaojing.wang
▴ 50 • written 8.8 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 8.8 years ago by
xiaojing.wang
▴ 50 • written 8.8 years ago by
kristenbeck527
• 0
0
votes
3
replies
1.7k
views
calculateRPKM error in customProDB
software error
customprodb
updated 2.4 years ago by
Anne
• 0 • written 6.7 years ago by
javamng
▴ 10
2
votes
2
replies
1.6k
views
customProDB: issues getting dbSNP data for human (hg19)
customprodb
dbsnp
refseq
varianttools
updated 8.8 years ago by
xiaojing.wang
▴ 50 • written 8.8 years ago by
kristenbeck527
• 0
1
vote
1
reply
1.4k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 2.4 years ago by
Anne
• 0 • written 6.7 years ago by
javamng
▴ 10
0
votes
0
replies
1.1k
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
7.7 years ago
yeh234
• 0
0
votes
1
reply
1.1k
views
customProDB, OutputVarproseq function update (snvproseq)
customprodb
updated 7.4 years ago by
xiaojing.wang
▴ 50 • written 7.4 years ago by
georges.bedran
• 0
0
votes
1
reply
1.1k
views
Pull request for customProDB package
customProDB
featurerequest
updated 7.9 years ago by
Dan Tenenbaum
★ 8.2k • written 7.9 years ago by
matt.chambers42
▴ 10
0
votes
1
reply
1.0k
views
CustomproDB JunctionType function
customprodb
updated 7.8 years ago by
xiaojing.wang
▴ 50 • written 7.8 years ago by
georges.bedran
• 0
0
votes
1
reply
934
views
aaVariation function bug (Methonine instead of Leucine)
customprodb
translation
updated 5.7 years ago by
xiaojing.wang
▴ 50 • written 6.0 years ago by
georges.bedran
• 0
0
votes
1
reply
922
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 5.6 years ago by
xiaojing.wang
▴ 50 • written 5.6 years ago by
iranmdl15
• 0
0
votes
0
replies
910
views
Annotation package generation error for customprodb for hg38
customprodb
6.2 years ago
arunima2
• 0
0
votes
1
reply
905
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 5.7 years ago by
xiaojing.wang
▴ 50 • written 5.8 years ago by
samupatt
• 0
0
votes
0
replies
779
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
21 months ago
04.marshal-decibel
• 0
0
votes
1
reply
775
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
4.8 years ago
Elena.M
• 0
0
votes
1
reply
744
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
4.5 years ago
laura.fancello
• 0
0
votes
1
reply
458
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 11 months ago by
James W. MacDonald
65k • written 11 months ago by
Esraa
• 0
0
votes
0
replies
447
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
20 months ago
04.marshal-decibel
• 0
0
votes
1
reply
435
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
10 months ago
Esraa
• 0
0
votes
0
replies
281
views
customProDB: error aberrant fasta from SNV
customProDB
15 months ago
finoa.li
• 0
21 results • Page
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Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
shuwangxinze1996
• 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough? Thank …
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
This comment helps.
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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