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customProDB
•
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0
votes
1
reply
700
views
customProDB easyrun error in generating a custom protein database: Error in keepSeqlevels(anno, seqlevels(galn), pruning.mode = "coarse")
customProDB
19 months ago
Esraa
• 0
0
votes
1
reply
703
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 21 months ago by
James W. MacDonald
67k • written 21 months ago by
Esraa
• 0
0
votes
0
replies
432
views
customProDB: error aberrant fasta from SNV
customProDB
2.0 years ago
finoa.li
• 0
0
votes
0
replies
635
views
CustomProDB: specify a snp dataset to be used for the SNP annotation
customProDB
2.5 years ago
04.marshal-decibel
• 0
0
votes
0
replies
1.0k
views
How to get the chrominfo from ENSEMBL? (biomaRt and customProDB)
biomaRt
customProDB
2.6 years ago
04.marshal-decibel
• 0
0
votes
1
reply
934
views
customProDB: function PrepareAnnotationEnsembl() not working (biomart issue?)
customProDB
Ensembl connection
biomart
5.2 years ago
laura.fancello
• 0
0
votes
1
reply
1.0k
views
CustomProDB InputVcf() - Issue getting the GRanges INDEL object from VCF file
vcf
snv
gatk
customprodb
inputvcf
5.6 years ago
Elena.M
• 0
4
votes
9
replies
3.9k
views
Create protein sequences including variants from a VCF file
VariantAnnotation
customProDB
updated 8 months ago by
Yun
• 0 • written 5.9 years ago by
daniel.magnus.bader
▴ 50
0
votes
1
reply
1.1k
views
customProDB: "complex" SNV scenarios handling
customprodb
updated 6.4 years ago by
xiaojing.wang
▴ 50 • written 6.4 years ago by
iranmdl15
• 0
0
votes
1
reply
1.2k
views
Error with PrepareAnnotationRefseq: "tablenametotrack2: UCSC table "refGene" is not supported"
customProDB
updated 6.5 years ago by
xiaojing.wang
▴ 50 • written 6.6 years ago by
samupatt
• 0
0
votes
1
reply
1.1k
views
aaVariation function bug (Methonine instead of Leucine)
customprodb
translation
updated 6.5 years ago by
xiaojing.wang
▴ 50 • written 6.8 years ago by
georges.bedran
• 0
0
votes
3
replies
1.9k
views
calculateRPKM error in customProDB
software error
customprodb
updated 3.2 years ago by
Anne
• 0 • written 7.5 years ago by
javamng
▴ 10
0
votes
0
replies
1.1k
views
Annotation package generation error for customprodb for hg38
customprodb
7.0 years ago
arunima2
• 0
1
vote
1
reply
1.6k
views
error with calculateRPKM in customProDB
customProDB
software error
updated 3.2 years ago by
Anne
• 0 • written 7.5 years ago by
javamng
▴ 10
0
votes
1
reply
1.2k
views
customProDB, OutputVarproseq function update (snvproseq)
customprodb
updated 8.1 years ago by
xiaojing.wang
▴ 50 • written 8.2 years ago by
georges.bedran
• 0
0
votes
0
replies
1.3k
views
PrepareAnnotationRefseq2 function error!
PGA
customprodb
8.5 years ago
yeh234
• 0
0
votes
1
reply
1.3k
views
CustomproDB JunctionType function
customprodb
updated 8.6 years ago by
xiaojing.wang
▴ 50 • written 8.6 years ago by
georges.bedran
• 0
0
votes
1
reply
1.3k
views
Pull request for customProDB package
customProDB
featurerequest
updated 8.7 years ago by
Dan Tenenbaum
★ 8.2k • written 8.7 years ago by
matt.chambers42
▴ 10
2
votes
4
replies
2.1k
views
customProDB: error aberrant fasta from indels
indel
customprodb
fasta
variantannotation
updated 9.6 years ago by
xiaojing.wang
▴ 50 • written 9.6 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 9.6 years ago by
xiaojing.wang
▴ 50 • written 9.6 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 9.6 years ago by
xiaojing.wang
▴ 50 • written 9.6 years ago by
kristenbeck527
• 0
21 results • Page
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Comment: Sample-specific methylation values using QSEA
by
User3088
• 0
Thanks Simon. I got the sample-specific methylation values by using '**samples=getSampleNames**' ``` result=makeTable(qs=prad_QSEAset, glm=…
Comment: input for singR function
by
iamin053
• 0
Hi Paria, I'm wondering if you were able to get an answer on this please. I would greatly appreciate any comments!
Comment: build samplesheet and plot profile
by
yf
• 0
![enter image description here][1] [1]: /media/images/8ea93bd0-bc90-443d-a332-4701f54a
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
Votes
Unused arguments error without used arguments in GSVA?
Answer: Is it always preferable to recount library sizes of DGEList object in edgeR afte
A: Doubt about the "zero expression" genes or genes with no reads at all in the co
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
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