Showing : genomicfeatures • reset
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(missing?) UCSCKG -> SYMBOL mappings in Homo.sapiens (etc.)
Organism GenomicFeatures Organism GenomicFeatures
updated 12.8 years ago by ★ 7.2k • written 12.8 years ago by ★ 4.2k
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2
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Extract Exon Features from GenomicFeatures Leads to Inconsistent Pairing of Gene and Exon IDs
GenomicFeatures GenomicFeatures
updated 12.9 years ago by ★ 13k • written 12.9 years ago by ▴ 320
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goseq: biased distribution of p-values
GO GenomicFeatures goseq GO GenomicFeatures goseq
13.0 years ago Joachim Jacob ▴ 10
0
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4
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3.8k
views
How can I extract promoter regions from a list NCBI genbank acc?
GenomicFeatures GenomicFeatures
updated 13.1 years ago by ★ 7.2k • written 13.1 years ago by ▴ 200
2
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7
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Extend GRanges start/end
Genetics GenomicFeatures Genetics GenomicFeatures
updated 13.1 years ago by ★ 11k • written 13.1 years ago by ▴ 510
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0
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450K annotation: discrepancy between GEO GPL and Bioconductor annotation
Annotation db0 probe annotate PROcess GenomicFeatures GenomicRanges Annotation db0 probe
13.1 years ago Marc Carlson ★ 7.2k
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1
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928
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creating transcriptDB from gff3 files
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 13.3 years ago by ★ 6.8k • written 13.3 years ago by ▴ 210
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[Engineers for ensemblgenomes.org #251937] BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info …
Drosophila melanogaster TranscriptDb biomaRt GenomicFeatures genomes Drosophila melanogaster
13.4 years ago Malcolm Cook ★ 1.6k
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1
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1.2k
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Finding coding SNPs with predictCoding
SNP Annotation BSgenome BSgenome GenomicFeatures cycle genomes SNP Annotation BSgenome
updated 13.5 years ago by ★ 1.7k • written 13.5 years ago by ★ 6.8k
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1
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1.3k
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VariantAnnotation locateVariants - meaning of precedesID and followsID
BSgenome TranscriptDb BSgenome GenomicFeatures BSgenome TranscriptDb BSgenome
updated 13.6 years ago by ★ 6.8k • written 13.6 years ago by ▴ 80
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1
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883
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VariantAnnotation's predictCoding (via getTranscriptSeqs) calls makeUCSCTxListFromGRangesList with wrong function signature?
GenomicFeatures GenomicFeatures
updated 13.6 years ago by ★ 6.8k • written 13.7 years ago by ▴ 230
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6
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[Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred f…
Cancer Organism biomaRt GenomicFeatures genomes Cancer Organism biomaRt GenomicFeatures
updated 13.7 years ago by ▴ 660 • written 13.7 years ago by 16k
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4
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Problem installing GenomicFeatures
GenomicFeatures GenomicFeatures
13.7 years ago Georg Otto ▴ 120
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0
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1.0k
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making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation GO Cancer BSgenome Biostrings BSgenome rtracklayer GenomicFeatures goseq GO
13.8 years ago Hervé Pagès 16k
0
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7
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1.7k
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GenomicFeatures::makeTranscriptDbFromGTF?
Cancer GenomicFeatures Cancer GenomicFeatures
updated 13.8 years ago by ★ 11k • written 13.8 years ago by ★ 13k
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3
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2.2k
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RE : maping SNPs
SNP Annotation Cancer SNPlocs TranscriptDb GenomicFeatures GenomicRanges SNP Annotation
updated 13.8 years ago by 16k • written 13.8 years ago by ▴ 450
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3
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[Hinxton #251937] RE: GenomicFeatures::makeTranscriptDbFromBiomart - BioMart data anomaly: for some transcripts, the cds cumulative length inferred f…
Cancer Organism biomaRt GenomicFeatures Cancer Organism biomaRt GenomicFeatures
updated 13.8 years ago by ▴ 660 • written 13.8 years ago by ★ 1.6k
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BioMart data anomaly: for some transcripts, the cds cumulative length inferred from the exon and UTR info doesn't match the "cds_length" attribute fr…
TranscriptDb biomaRt GenomicFeatures TranscriptDb biomaRt GenomicFeatures
13.8 years ago Malcolm Cook ★ 1.6k
0
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1
reply
943
views
subsetting transcriptDb
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 13.8 years ago by ★ 7.2k • written 13.8 years ago by ▴ 360
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1
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1.2k
views
intragenic sequence extraction
Annotation Cancer Organism BSgenome BSgenome GenomicFeatures Annotation Cancer Organism
updated 14.0 years ago by ★ 13k • written 14.0 years ago by ▴ 90
0
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1
reply
1.3k
views
GenomicFeatures more detail.
SNP annotate GenomicFeatures SNP annotate GenomicFeatures
updated 14.5 years ago by ★ 6.8k • written 14.5 years ago by ▴ 970
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4
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views
Get all 3'utr and 5'utr region from GenomicFeatures
GenomicFeatures GenomicFeatures
updated 14.5 years ago by 68k • written 14.5 years ago by ▴ 970
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5
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4.5k
views
Fast way to find which gene a snp located.
SNP GenomicFeatures SNP GenomicFeatures
updated 14.6 years ago by ▴ 10 • written 14.6 years ago by ▴ 970
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0
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1.3k
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inconsistency between GRangesList and transcriptDB object.
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
14.6 years ago zhenjiang xu ▴ 10
0
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13
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3.7k
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multiple hits with countOverlaps function
Sequencing GenomicFeatures Sequencing GenomicFeatures
14.6 years ago Wei Shi ★ 3.6k
0
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7
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2.3k
views
Mapping genomic coordinates to transcript coordinates? (revived)
Biostrings GenomicFeatures Biostrings GenomicFeatures
updated 14.7 years ago by ★ 11k • written 14.7 years ago by 16k
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3
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1.4k
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GenomicFeatures: makeGeneDbFromBiomart()
Annotation biomaRt GenomicFeatures Annotation biomaRt GenomicFeatures
updated 14.7 years ago by ★ 7.2k • written 14.7 years ago by ★ 4.1k
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9
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2.5k
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Mapping microarray probes to the genome using findOverlaps
Microarray Alignment Annotation zebrafish probe Biostrings GenomicFeatures Microarray
updated 14.8 years ago by 21k • written 14.8 years ago by 16k
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1
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1.1k
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Mapping genomic coordinates to transcript coordinates? (revived)
GenomicFeatures GenomicFeatures
updated 14.8 years ago by ▴ 90 • written 14.8 years ago by ★ 1.6k
0
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2
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1.8k
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RE : RE : maping SNPs
SNP SNPlocs TranscriptDb IRanges GenomicFeatures SNP SNPlocs TranscriptDb IRanges
updated 14.9 years ago by ★ 6.8k • written 14.9 years ago by ▴ 450
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0
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1.9k
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RE : maping SNPs; first foundation challenge offered
SNP Annotation Cancer SNPlocs TranscriptDb biomaRt GenomicFeatures SNP Annotation Cancer
14.9 years ago Vincent J. Carey, Jr. 6.7k
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2
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IRanges, GenomicRanges, GenomicFeatures?
Coverage Annotation TranscriptDb convert GenomicFeatures Coverage Annotation TranscriptDb
updated 15.1 years ago by ★ 13k • written 15.1 years ago by ▴ 60
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1
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1.2k
views
Problem with genomicFeatures: id2name
BSgenome biomaRt BSgenome GenomicFeatures BSgenome biomaRt BSgenome GenomicFeatures
updated 15.2 years ago by ★ 7.2k • written 15.2 years ago by ▴ 970
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Flagging overlapping gene exons (was Re: Question about CSAMA10 ...)
Annotation Cancer IRanges GenomicFeatures GenomicRanges Annotation Cancer IRanges
15.2 years ago Steve Lianoglou ★ 13k
2
votes
3
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2.6k
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How to get position for each gene ID/gene symbol instead of position for each transcript
Organism PROcess biomaRt GenomicFeatures Organism PROcess biomaRt GenomicFeatures
updated 15.3 years ago by ★ 13k • written 15.3 years ago by ★ 1.0k
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4
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1.5k
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Error mapping RNA-seq data to genome
GenomicFeatures GenomicRanges GenomicFeatures GenomicRanges
updated 15.3 years ago by 25k • written 15.3 years ago by ★ 1.3k
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0
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2.0k
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GenomicFeatures makeTranscriptDbFromUCSC on refGene supported?
Visualization rtracklayer GenomicFeatures Visualization rtracklayer GenomicFeatures
15.4 years ago Erik van den Akker ▴ 50
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6
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2.1k
views
GenomicFeatures: makeTranscriptDbFromUCSC on "refGene" supported?
rtracklayer GenomicFeatures rtracklayer GenomicFeatures
updated 15.4 years ago by 6.7k • written 15.4 years ago by ▴ 50
0
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1
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1.4k
views
is database RefSeq achievable from any Bioconductor package
Annotation Cancer biomaRt GenomicFeatures Annotation Cancer biomaRt GenomicFeatures
updated 15.5 years ago by ★ 6.5k • written 15.5 years ago by ★ 13k
0
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3
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1.1k
views
GenomicFeatures.Hsapiens.UCSC.hg19
GenomicFeatures GenomicFeatures
updated 15.6 years ago by ▴ 200 • written 15.6 years ago by ▴ 140
0
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2
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1.5k
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GenomicFeatures question
GenomicFeatures GenomicFeatures
updated 15.7 years ago by 6.7k • written 15.7 years ago by ▴ 970
291 results • Page 6 of 6
Recent ...
Replies
Comment: upstream git branches of bioc-release by TrentonCollier99 • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments. https://bioc-release.r-univ…
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much! will take that into consideration
Comment: Large logFC but somewhat high FDR by JKim • 0
Thank you very much for taking the time to answer the question. I really appreciate your insights and comments.
Comment: upstream git branches of bioc-release by Jeroen ▴ 10
OK I have updated https://bioc-release.r-universe.dev accordingly. Let me know if you find version differences when mirroring binaries.
Comment: Large logFC but somewhat high FDR by Gordon Smyth 53k
I don't know what `tp1` is. The relevant histogram would be: ``` hist(fit2$p.value[,"KO_vs_WT"]) ```
Votes
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
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