Showing : GenomicFeatures • reset
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(missing?) UCSCKG -> SYMBOL mappings in Homo.sapiens (etc.)
Organism GenomicFeatures Organism GenomicFeatures
updated 12.7 years ago by ★ 7.2k • written 12.7 years ago by ★ 4.2k
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Extract Exon Features from GenomicFeatures Leads to Inconsistent Pairing of Gene and Exon IDs
GenomicFeatures GenomicFeatures
updated 12.8 years ago by ★ 13k • written 12.8 years ago by ▴ 320
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goseq: biased distribution of p-values
GO GenomicFeatures goseq GO GenomicFeatures goseq
12.9 years ago Joachim Jacob ▴ 10
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4
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3.8k
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How can I extract promoter regions from a list NCBI genbank acc?
GenomicFeatures GenomicFeatures
updated 13.0 years ago by ★ 7.2k • written 13.0 years ago by ▴ 200
2
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7
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Extend GRanges start/end
Genetics GenomicFeatures Genetics GenomicFeatures
updated 13.0 years ago by ★ 11k • written 13.0 years ago by ▴ 510
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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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916
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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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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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VariantAnnotation's predictCoding (via getTranscriptSeqs) calls makeUCSCTxListFromGRangesList with wrong function signature?
GenomicFeatures GenomicFeatures
updated 13.6 years ago by ★ 6.8k • written 13.6 years ago by ▴ 230
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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 13.6 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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996
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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
13.7 years ago Hervé Pagès 16k
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7
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1.7k
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GenomicFeatures::makeTranscriptDbFromGTF?
Cancer GenomicFeatures Cancer GenomicFeatures
updated 13.7 years ago by ★ 11k • written 13.7 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 13.7 years ago by 16k • written 13.7 years ago by ▴ 450
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3
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1.4k
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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 13.7 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
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929
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 13.9 years ago by ★ 13k • written 13.9 years ago by ▴ 90
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1
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1.3k
views
GenomicFeatures more detail.
SNP annotate GenomicFeatures SNP annotate GenomicFeatures
updated 14.4 years ago by ★ 6.8k • written 14.4 years ago by ▴ 970
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4
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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
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Fast way to find which gene a snp located.
SNP GenomicFeatures SNP GenomicFeatures
updated 14.5 years ago by ▴ 10 • written 14.5 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
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13
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3.6k
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multiple hits with countOverlaps function
Sequencing GenomicFeatures Sequencing GenomicFeatures
14.6 years ago Wei Shi ★ 3.6k
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7
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2.3k
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Mapping genomic coordinates to transcript coordinates? (revived)
Biostrings GenomicFeatures Biostrings GenomicFeatures
updated 14.6 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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2.4k
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Mapping microarray probes to the genome using findOverlaps
Microarray Alignment Annotation zebrafish probe Biostrings GenomicFeatures Microarray
updated 14.7 years ago by 21k • written 14.7 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 14.7 years ago by ▴ 90 • written 14.7 years ago by ★ 1.6k
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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 14.8 years ago by ★ 6.8k • written 14.8 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 15.0 years ago by ★ 13k • written 15.0 years ago by ▴ 60
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1
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1.2k
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Problem with genomicFeatures: id2name
BSgenome biomaRt BSgenome GenomicFeatures BSgenome biomaRt BSgenome GenomicFeatures
updated 15.1 years ago by ★ 7.2k • written 15.1 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
15.1 years ago Steve Lianoglou ★ 13k
2
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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 15.2 years ago by ★ 13k • written 15.2 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 15.2 years ago by 25k • written 15.2 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
15.3 years ago Erik van den Akker ▴ 50
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6
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2.1k
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GenomicFeatures: makeTranscriptDbFromUCSC on "refGene" supported?
rtracklayer GenomicFeatures rtracklayer GenomicFeatures
updated 15.3 years ago by 6.7k • written 15.3 years ago by ▴ 50
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1
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1.4k
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is database RefSeq achievable from any Bioconductor package
Annotation Cancer biomaRt GenomicFeatures Annotation Cancer biomaRt GenomicFeatures
updated 15.4 years ago by ★ 6.5k • written 15.4 years ago by ★ 13k
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3
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1.1k
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GenomicFeatures.Hsapiens.UCSC.hg19
GenomicFeatures GenomicFeatures
updated 15.5 years ago by ▴ 200 • written 15.5 years ago by ▴ 140
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2
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1.5k
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GenomicFeatures question
GenomicFeatures GenomicFeatures
updated 15.6 years ago by 6.7k • written 15.6 years ago by ▴ 970
291 results • Page 6 of 6
Recent ...
Replies
Answer: "Watched Tags" are being erased rather than updated by shepherl 4.2k
This should now be resolved
Answer: Question about collapsing ASVs by genus level during DESeq2 analysis by Michael Love 43k
I'll just note that microbiome stats folks tend to use other tools than DESeq2. > several ASVs belong to the same genus but are not iden…
Comment: Integration: Paired-end vs healthy single-end from a different source by igkryycpinmshzugby • 0
Yes, Option 1 (technical homogenization) reprocessing paired-end samples as single-end using only R1 is the most defensible approach when l…
Answer: Integration: Paired-end vs healthy single-end from a different source by James W. MacDonald 68k
If by reprocess you mean generate libraries and re-sequence, then that's something you could do. Otherwise the biological and technical dif…
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112
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Bioconductor 3.22 Released!
Bioconductor 3.22 Released!
Comment: "Watched Tags" are being erased rather than updated
Comment: deseq2 filter the low counts
Answer: DESeq2 interactions
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