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GenomicFeatures
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0
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0
replies
1.0k
views
Extract Exon Features from GenomicFeatures Leads to Inconsistent Pairing of Gene and Exon IDs
Cancer
GenomicFeatures
Cancer
GenomicFeatures
13.0 years ago
Hervé Pagès
16k
0
votes
1
reply
1.6k
views
(missing?) UCSCKG -> SYMBOL mappings in Homo.sapiens (etc.)
Organism
GenomicFeatures
Organism
GenomicFeatures
updated 13.0 years ago by
Marc Carlson
★ 7.2k • written 13.0 years ago by
Tim Triche
★ 4.2k
0
votes
2
replies
1.3k
views
Extract Exon Features from GenomicFeatures Leads to Inconsistent Pairing of Gene and Exon IDs
GenomicFeatures
GenomicFeatures
updated 13.1 years ago by
Steve Lianoglou
★ 13k • written 13.1 years ago by
Fong Chun Chan
▴ 320
0
votes
0
replies
1.1k
views
goseq: biased distribution of p-values
GO
GenomicFeatures
goseq
GO
GenomicFeatures
goseq
13.2 years ago
Joachim Jacob
▴ 10
0
votes
4
replies
4.0k
views
How can I extract promoter regions from a list NCBI genbank acc?
GenomicFeatures
GenomicFeatures
updated 13.3 years ago by
Marc Carlson
★ 7.2k • written 13.3 years ago by
Yisong Zhen
▴ 200
2
votes
7
replies
6.0k
views
Extend GRanges start/end
Genetics
GenomicFeatures
Genetics
GenomicFeatures
updated 13.3 years ago by
Michael Lawrence
★ 11k • written 13.3 years ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
0
replies
1.9k
views
450K annotation: discrepancy between GEO GPL and Bioconductor annotation
Annotation
db0
probe
annotate
PROcess
GenomicFeatures
GenomicRanges
Annotation
db0
probe
13.3 years ago
Marc Carlson
★ 7.2k
0
votes
1
reply
970
views
creating transcriptDB from gff3 files
TranscriptDb
GenomicFeatures
TranscriptDb
GenomicFeatures
updated 13.5 years ago by
Valerie Obenchain
★ 6.8k • written 13.5 years ago by
gowtham
▴ 210
0
votes
0
replies
1.6k
views
[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
13.6 years ago
Malcolm Cook
★ 1.6k
0
votes
1
reply
1.2k
views
Finding coding SNPs with predictCoding
SNP
Annotation
BSgenome
BSgenome
GenomicFeatures
cycle
genomes
SNP
Annotation
BSgenome
updated 13.7 years ago by
Thomas Girke
★ 1.7k • written 13.7 years ago by
Valerie Obenchain
★ 6.8k
0
votes
1
reply
1.4k
views
VariantAnnotation locateVariants - meaning of precedesID and followsID
BSgenome
TranscriptDb
BSgenome
GenomicFeatures
BSgenome
TranscriptDb
BSgenome
updated 13.8 years ago by
Valerie Obenchain
★ 6.8k • written 13.8 years ago by
Paul Theodor Pyl
▴ 80
0
votes
1
reply
932
views
VariantAnnotation's predictCoding (via getTranscriptSeqs) calls makeUCSCTxListFromGRangesList with wrong function signature?
GenomicFeatures
GenomicFeatures
updated 13.8 years ago by
Valerie Obenchain
★ 6.8k • written 13.8 years ago by
Sang Chul Choi
▴ 230
0
votes
6
replies
2.1k
views
[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 13.9 years ago by
Rhoda Kinsella
▴ 660 • written 13.9 years ago by
Hervé Pagès
16k
0
votes
4
replies
6.0k
views
Problem installing GenomicFeatures
GenomicFeatures
GenomicFeatures
13.9 years ago
Georg Otto
▴ 120
0
votes
0
replies
1.0k
views
making use of the Apis mellifera BeeBase assembly 4 data in goseq
Annotation
GO
Cancer
BSgenome
Biostrings
BSgenome
rtracklayer
GenomicFeatures
goseq
GO
14.0 years ago
Hervé Pagès
16k
0
votes
7
replies
1.8k
views
GenomicFeatures::makeTranscriptDbFromGTF?
Cancer
GenomicFeatures
Cancer
GenomicFeatures
updated 14.0 years ago by
Michael Lawrence
★ 11k • written 14.0 years ago by
Steve Lianoglou
★ 13k
0
votes
3
replies
2.3k
views
RE : maping SNPs
SNP
Annotation
Cancer
SNPlocs
TranscriptDb
GenomicFeatures
GenomicRanges
SNP
Annotation
updated 14.0 years ago by
Hervé Pagès
16k • written 14.0 years ago by
SimonNoël
▴ 450
0
votes
3
replies
1.4k
views
[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 14.0 years ago by
Rhoda Kinsella
▴ 660 • written 14.0 years ago by
Malcolm Cook
★ 1.6k
0
votes
0
replies
1.6k
views
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
14.0 years ago
Malcolm Cook
★ 1.6k
0
votes
1
reply
970
views
subsetting transcriptDb
TranscriptDb
GenomicFeatures
TranscriptDb
GenomicFeatures
updated 14.0 years ago by
Marc Carlson
★ 7.2k • written 14.0 years ago by
Juliet Hannah
▴ 360
0
votes
1
reply
1.2k
views
intragenic sequence extraction
Annotation
Cancer
Organism
BSgenome
BSgenome
GenomicFeatures
Annotation
Cancer
Organism
updated 14.2 years ago by
Steve Lianoglou
★ 13k • written 14.2 years ago by
Yating Cheng
▴ 90
0
votes
1
reply
1.4k
views
GenomicFeatures more detail.
SNP
annotate
GenomicFeatures
SNP
annotate
GenomicFeatures
updated 14.7 years ago by
Valerie Obenchain
★ 6.8k • written 14.7 years ago by
Fabrice Tourre
▴ 970
0
votes
4
replies
4.5k
views
Get all 3'utr and 5'utr region from GenomicFeatures
GenomicFeatures
GenomicFeatures
updated 14.7 years ago by
James W. MacDonald
68k • written 14.7 years ago by
Fabrice Tourre
▴ 970
0
votes
5
replies
4.6k
views
Fast way to find which gene a snp located.
SNP
GenomicFeatures
SNP
GenomicFeatures
updated 14.7 years ago by
hind
▴ 10 • written 14.8 years ago by
Fabrice Tourre
▴ 970
0
votes
0
replies
1.3k
views
inconsistency between GRangesList and transcriptDB object.
TranscriptDb
GenomicFeatures
TranscriptDb
GenomicFeatures
14.8 years ago
zhenjiang xu
▴ 10
0
votes
13
replies
3.8k
views
multiple hits with countOverlaps function
Sequencing
GenomicFeatures
Sequencing
GenomicFeatures
14.8 years ago
Wei Shi
★ 3.6k
0
votes
7
replies
2.4k
views
Mapping genomic coordinates to transcript coordinates? (revived)
Biostrings
GenomicFeatures
Biostrings
GenomicFeatures
updated 14.9 years ago by
Michael Lawrence
★ 11k • written 14.9 years ago by
Hervé Pagès
16k
0
votes
3
replies
1.5k
views
GenomicFeatures: makeGeneDbFromBiomart()
Annotation
biomaRt
GenomicFeatures
Annotation
biomaRt
GenomicFeatures
updated 14.9 years ago by
Marc Carlson
★ 7.2k • written 14.9 years ago by
Guido Hooiveld
★ 4.1k
0
votes
9
replies
2.5k
views
Mapping microarray probes to the genome using findOverlaps
Microarray
Alignment
Annotation
zebrafish
probe
Biostrings
GenomicFeatures
Microarray
updated 14.9 years ago by
Sean Davis
21k • written 14.9 years ago by
Hervé Pagès
16k
0
votes
1
reply
1.2k
views
Mapping genomic coordinates to transcript coordinates? (revived)
GenomicFeatures
GenomicFeatures
updated 15.0 years ago by
Chris Fields
▴ 90 • written 15.0 years ago by
Malcolm Cook
★ 1.6k
0
votes
2
replies
1.9k
views
RE : RE : maping SNPs
SNP
SNPlocs
TranscriptDb
IRanges
GenomicFeatures
SNP
SNPlocs
TranscriptDb
IRanges
updated 15.1 years ago by
Valerie Obenchain
★ 6.8k • written 15.1 years ago by
SimonNoël
▴ 450
0
votes
0
replies
2.0k
views
RE : maping SNPs; first foundation challenge offered
SNP
Annotation
Cancer
SNPlocs
TranscriptDb
biomaRt
GenomicFeatures
SNP
Annotation
Cancer
15.1 years ago
Vincent J. Carey, Jr.
6.7k
0
votes
2
replies
1.2k
views
IRanges, GenomicRanges, GenomicFeatures?
Coverage
Annotation
TranscriptDb
convert
GenomicFeatures
Coverage
Annotation
TranscriptDb
updated 15.3 years ago by
Steve Lianoglou
★ 13k • written 15.3 years ago by
Oleg Moskvin
▴ 60
0
votes
1
reply
1.3k
views
Problem with genomicFeatures: id2name
BSgenome
biomaRt
BSgenome
GenomicFeatures
BSgenome
biomaRt
BSgenome
GenomicFeatures
updated 15.4 years ago by
Marc Carlson
★ 7.2k • written 15.4 years ago by
Paul Leo
▴ 970
0
votes
0
replies
1.4k
views
Flagging overlapping gene exons (was Re: Question about CSAMA10 ...)
Annotation
Cancer
IRanges
GenomicFeatures
GenomicRanges
Annotation
Cancer
IRanges
15.4 years ago
Steve Lianoglou
★ 13k
2
votes
3
replies
2.7k
views
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 15.5 years ago by
Steve Lianoglou
★ 13k • written 15.5 years ago by
shirley zhang
★ 1.0k
0
votes
4
replies
1.5k
views
Error mapping RNA-seq data to genome
GenomicFeatures
GenomicRanges
GenomicFeatures
GenomicRanges
updated 15.5 years ago by
Martin Morgan
25k • written 15.5 years ago by
Paul Geeleher
★ 1.3k
0
votes
0
replies
2.0k
views
GenomicFeatures makeTranscriptDbFromUCSC on refGene supported?
Visualization
rtracklayer
GenomicFeatures
Visualization
rtracklayer
GenomicFeatures
15.6 years ago
Erik van den Akker
▴ 50
0
votes
6
replies
2.1k
views
GenomicFeatures: makeTranscriptDbFromUCSC on "refGene" supported?
rtracklayer
GenomicFeatures
rtracklayer
GenomicFeatures
updated 15.6 years ago by
Vincent J. Carey, Jr.
6.7k • written 15.6 years ago by
Erik van den Akker
▴ 50
0
votes
1
reply
1.4k
views
is database RefSeq achievable from any Bioconductor package
Annotation
Cancer
biomaRt
GenomicFeatures
Annotation
Cancer
biomaRt
GenomicFeatures
updated 15.7 years ago by
Kasper Daniel Hansen
★ 6.5k • written 15.7 years ago by
Steve Lianoglou
★ 13k
0
votes
3
replies
1.1k
views
GenomicFeatures.Hsapiens.UCSC.hg19
GenomicFeatures
GenomicFeatures
updated 15.8 years ago by
burak kutlu
▴ 200 • written 15.8 years ago by
Burak Kutlu
▴ 140
0
votes
2
replies
1.5k
views
GenomicFeatures question
GenomicFeatures
GenomicFeatures
updated 15.9 years ago by
Vincent J. Carey, Jr.
6.7k • written 15.9 years ago by
Paul Leo
▴ 970
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