Showing : variantannotation • reset
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2
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120
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Docker usage with Trio Bioconductor Package
VariantAnnotation docker trio
updated 15 days ago by ★ 2.8k • written 15 days ago by • 0
4
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8
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443
views
TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene
MetID TxDB.Hsapiens.UCSC.hg38.knownGene locateVariants GenomicFeatures VariantAnnotation
10 weeks ago • updated 9 weeks ago davidhillis • 0
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0
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184
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VariantAnnotation::readVcf incorrectly processes GATK Mutect2 vcf INFO field AS_SB_TABLE
vcf AS_SB_TABLE readVcf Mutect2 VariantAnnotation
3 months ago therealgenna • 0
0
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3
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353
views
Add GP values to VCF
VariantAnnotation
4 months ago Stephanie M. Gogarten ▴ 840
0
votes
1
reply
595
views
Confused about understanding the output and statistics of BAM file after STAR aligning
RNAseq123 VariantFiltering Alignment VariantAnnotation
updated 6 months ago by 62k • written 6 months ago by ▴ 10
2
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4
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441
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
8 months ago rwan.work • 0
0
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2
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279
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
8 months ago rwan.work • 0
0
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2
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2.1k
views
merging VCF files
VariantAnnotation VariantAnnotation VariantAnnotation VariantAnnotation
written 10.4 years ago by ▴ 840
0
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3
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663
views
Problem with intronic variants in VariantAnnotation
VariantAnnotation
updated 15 months ago by • 0 • written 17 months ago by • 0
0
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2
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549
views
Reading vcf file with readVcf
VariantAnnotation
20 months ago aurelien.dejode • 0
0
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2
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471
views
Multiple exons for predictCoding() from VariantAnnotation (use phase information from gff3 file)?
VariantAnnotation
updated 21 months ago by 16k • written 22 months ago by • 0
0
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5
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819
views
installation error: Error in setIs(class2, cli, extensionObject = obji, doComplete = FALSE and setClass() for chromVAR and VariantAnnotation
Install VariantAnnotation Bioconductor chromVAR
updated 21 months ago by 6.6k • written 21 months ago by • 0
0
votes
1
reply
494
views
GRanges object out-of-bound
VariantAnnotation
updated 21 months ago by 6.6k • written 22 months ago by • 0
2
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3
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666
views
readVcf(remoteFile, "hg19", "region") works on macos, fails on linux and in docker
open.BcfFile VariantAnnotation
updated 18 months ago by • 0 • written 22 months ago by ▴ 470
0
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0
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359
views
Annotate mutations on DNA level to splice transcripts
VariantAnnotation
22 months ago Kasper_holm2 • 0
0
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4
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815
views
Error of read in large vcf file using readVcf
SomaticSignatures VariantAnnotation
updated 23 months ago by 62k • written 23 months ago by • 0
0
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2
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739
views
VariantAnnotation::readVcf not reading variants
VariantAnnotation
updated 2.0 years ago by 62k • written 2.0 years ago by • 0
0
votes
2
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1.5k
views
VCF File too large for tabix. Best option to make it usable with R?
samtools tabix VariantAnnotation VCFArray
updated 2.2 years ago by 6.6k • written 2.2 years ago by • 0
1
vote
12
replies
1.9k
views
readVcf does not recognize tabix index
VariantAnnotation readvcf tabix
updated 2.2 years ago by 6.6k • written 2.2 years ago by • 0
0
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2
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695
views
readVCF requires the argument "genome". What does it stand for?
Genome readVcf VariantAnnotation
2.2 years ago naive • 0
2
votes
1
reply
770
views
Matching Variants Between Two VCF Objects
VariantAnnotation
updated 2.5 years ago by ▴ 100 • written 2.5 years ago by ★ 1.5k
2
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2
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688
views
Obtaining Comments From VCF Header
VariantAnnotation VCFHeader
updated 2.9 years ago by 25k • written 2.9 years ago by ★ 1.5k
3
votes
2
replies
794
views
Import or Subset VCF PASS Variants
VariantAnnotation subset ScanVcfParam
updated 3.1 years ago by 25k • written 3.1 years ago by ★ 1.5k
0
votes
2
replies
708
views
Extract structural variant and flanking sequence from VCF and fasta, in R
VariantAnnotation Bioconductor VCF Structural variants R
updated 3.1 years ago by 25k • written 3.1 years ago by • 0
0
votes
1
reply
371
views
Can strand be set to minus in VRanges objects?
VariantAnnotation
updated 3.4 years ago by 62k • written 3.4 years ago by • 0
0
votes
1
reply
713
views
FilterVCF Filter '' failed: shape of 'skeleton' is not compatible with 'NROW(flesh)'
variantAnnotation
updated 3.6 years ago by 25k • written 3.6 years ago by • 0
2
votes
3
replies
1.0k
views
"Packages required but not available." rtracklayer in OSX is not available to CRAN, resulting in errors for downstream dependencies.
GenomicRanges rtracklayer VariantAnnotation S4Vectors SummarizedExperiment
updated 3.9 years ago by 13k • written 3.9 years ago by ▴ 30
2
votes
3
replies
545
views
VariantAnnotation - subset multi-allele variants
variantAnnotation
updated 3.9 years ago by 11k • written 3.9 years ago by • 0
0
votes
1
reply
494
views
negative AD value interfering with readVcfasVRanges
VariantAnnotation
updated 3.9 years ago by 11k • written 4.0 years ago by • 0
0
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3
replies
677
views
rbind VCF Two Objects Column Names Error
VariantAnnotation VCF
4.0 years ago Dario Strbenac ★ 1.5k
0
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0
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527
views
predictCoding warning message: serious or not?
software error annotation VariantAnnotation
updated 4.2 years ago by 3.5k • written 4.2 years ago by • 0
2
votes
3
replies
986
views
Error in VCF parsing with VariantAnnotation
software error VariantAnnotation ensemblVEP
updated 4.2 years ago by ★ 6.7k • written 4.2 years ago by ▴ 20
3
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8
replies
2.0k
views
Create protein sequences including variants from a VCF file
VariantAnnotation customProDB
4.2 years ago daniel.magnus.bader ▴ 40
0
votes
1
reply
696
views
VariantAnnotation fails to load VCF record
variantannotation
4.5 years ago Daniel Cameron ▴ 40
0
votes
6
replies
1.1k
views
How to prepare .vcf for seqCAT
seqCAT variantannotation gatk
updated 4.5 years ago by ▴ 30 • written 4.5 years ago by • 0
0
votes
1
reply
584
views
writeVcf save invalid vcf with metadata out of order
variantannotation
updated 4.5 years ago by ★ 6.7k • written 4.5 years ago by ▴ 20
1
vote
7
replies
2.4k
views
Data from ##SAMPLE lines in VCF?
variantannotation coldata
updated 4.7 years ago by ★ 6.7k • written 4.7 years ago by ▴ 10
3
votes
3
replies
882
views
Get rs numbers using IntronVariants() in VariantAnnotation, locateVariants
variantannotation
updated 4.9 years ago by ★ 6.7k • written 4.9 years ago by ▴ 10
3
votes
4
replies
1.2k
views
Problem when transforming Platypus vcf to VRanges
variantannotation vcf readvcf vranges
updated 4.9 years ago by 11k • written 4.9 years ago by • 0
0
votes
2
replies
832
views
Error: invalid class "VRanges" object
variantannotation VRanges R Rle
updated 4.9 years ago by ★ 6.7k • written 4.9 years ago by • 0
0
votes
2
replies
905
views
VariantAnnotation::locateVariants error coming from XVector
variantannotation xvector iranges
5.0 years ago Vivek.b ▴ 100
0
votes
2
replies
1.1k
views
filtering a VCF file based on genotype
variantannotation
updated 5.0 years ago by ★ 6.7k • written 5.0 years ago by ▴ 660
0
votes
1
reply
768
views
VariantAnnotation and filtering a VCF
variantannotation
5.1 years ago Bogdan ▴ 660
0
votes
1
reply
784
views
Annotating outdated SNP identifiers
variants variantannotation SNPlocs.Hsapiens.dbSNP150.GRCh38 biomaRt
5.2 years ago sandmann.t ▴ 70
2
votes
2
replies
982
views
[VariantAnnotation] Preserve query metadata with locateVariants()
variantannotation locatevariants metadata mcols
updated 5.4 years ago by ★ 6.7k • written 5.4 years ago by ▴ 660
0
votes
2
replies
2.5k
views
Problem using biocLite() to update packages
biocLite BiocInstaller variantannotation
updated 5.5 years ago by 62k • written 5.5 years ago by ★ 2.0k
0
votes
1
reply
927
views
predictCoding errors with: sequence ^1$ not found
variantannotation predict coding locateVariants granges
5.6 years ago tony j • 0
7
votes
4
replies
1.6k
views
BiocGenerics built with R 3.4.2 changes behaviour
biocgenerics iranges variantannotation
updated 5.6 years ago by 16k • written 5.7 years ago by ▴ 40
7
votes
6
replies
1.4k
views
SNP location annotation problem in "VariantAnnotation" package
annotation variantannotation
updated 5.7 years ago by ★ 6.7k • written 5.7 years ago by ▴ 20
0
votes
4
replies
1.3k
views
Translation Error in predictCoding() for VariantAnnotation
VariantAnnotation
updated 5.7 years ago by 16k • written 5.7 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: DESeq2 or edgeR for Presence and Absence of Proteins by ATpoint ★ 2.8k
No, both tools expect count data with certain distributional assumptions which are not satisfied by binary data. Since you're a master …
Comment: Visualization of negative log CPM values by Gordon Smyth 47k
Sorry, but some of the things you say are not correct. > compound B has 2 statistically significant genes that are up-regulated No, there…
Comment: Visualization of negative log CPM values by ATpoint ★ 2.8k
Applies to both.
Comment: Visualization of negative log CPM values by Sabiha ▴ 10
@atpoint OK, are you referring to the `log2(cpm+1)` or `log2(tpm+1)`
Comment: Visualization of negative log CPM values by Sabiha ▴ 10
@gordonsmyth noted. Related to the graphs above, the table below is the output from `limma`, and compound B has 2 statistically significant…
Votes
Answer: DESeq2 or edgeR for Presence and Absence of Proteins
Comment: Visualization of negative log CPM values
Any efficient workaround to identify highly variable genes in Affymetrix microarray expression data?
Filtering low intensity probes in microarray data
Comment: Visualization of negative log CPM values
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