Showing : GenomicFeatures • reset
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makeTxDbFromGFF not capturing/displaying 'gene' records from GFF3 file.
genomicfeatures makeTxDbFromGFF
updated 10.5 years ago by 16k • written 10.5 years ago by • 0
1
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7
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6.9k
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Existence of a makeTxDbFromGFF function in GenomicFeatures package?
genomicfeatures
10.6 years ago • updated 10.5 years ago pterry • 0
0
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2
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8.8k
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Error with "library("GenomicFeatures")" - "there is no package called ‘XML’"
genomicfeatures xml loadnamespace
10.5 years ago greg.mulhearn • 0
3
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7
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2.6k
views
Add up RLEs that are in lists?
RLE GenomicFeatures rnaseq
updated 10.6 years ago by 16k • written 10.6 years ago by ▴ 30
3
votes
10
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5.7k
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Getting a list of all tRNA encoding genes for an organism?
trna ncrna genomicfeatures featuredb biomart
updated 10.6 years ago by 16k • written 10.6 years ago by ▴ 180
5
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3
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2.8k
views
Feature types in TxDb objects
GenomicFeatures rtracklayer
10.7 years ago • updated 10.6 years ago Thomas Girke ★ 1.7k
0
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1
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1.5k
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Mean Coverage version of stat_coverage and coverage?
grangeslist granges Genomicfeatures bam
10.6 years ago gen ▴ 30
0
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4
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1.7k
views
Error in makeTranscriptDbFromGFF
deseq2 genomicfeatures
updated 10.6 years ago by 16k • written 10.6 years ago by • 0
2
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1
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1.2k
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Plot coverage in a presentation for GenomicFeatures
genomicfeatures
updated 10.6 years ago by ★ 11k • written 10.6 years ago by ▴ 20
3
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4
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2.3k
views
Introns at transcript expression level
genomicfeatures iranges
updated 10.6 years ago by 16k • written 10.6 years ago by ▴ 20
0
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7
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2.3k
views
Speeding up or replacing Loops to process Bam Reads
genomicranges reads genomicfeatures Bam
10.6 years ago gen ▴ 30
2
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13
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3.2k
views
makeTranscriptDbFromBiomart failure from Data Anomaly
biomart genomicfeatures
updated 10.6 years ago by 16k • written 10.6 years ago by ▴ 80
0
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9
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4.6k
views
genomicfeatures rsqlite database or disk is full
genomicfeatures
updated 10.6 years ago by ★ 7.2k • written 10.6 years ago by ▴ 90
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3
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1.4k
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Problem with mcols in GenomicFeatures
genomicfeatures
10.7 years ago Jake ▴ 90
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8
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2.9k
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makeTranscriptDbFromGFF Unexpected transcript duplicates
genomicfeatures
10.7 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
2
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16
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5.0k
views
TxDb annotations for human chrM
GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene annotation
10.8 years ago • updated 10.7 years ago Robert Castelo ★ 3.4k
0
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1
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1.3k
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summarizeOverlaps on partial BAM file?
GenomicFeatures GRange Rsamtools
updated 10.8 years ago by ★ 6.8k • written 10.8 years ago by • 0
3
votes
2
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2.1k
views
Problem with TxDb.Mmusculus.UCSC.mm9.knownGene
software error txdb.mmusculus.ucsc.mm9.knowngene genomicfeatures
updated 10.8 years ago by 16k • written 10.8 years ago by • 0
0
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1
reply
1.5k
views
Get exonFrames metadata from makeTranscriptDbFromUCSC command
genomicfeatures genomicranges ucsc
updated 10.8 years ago by 16k • written 10.8 years ago by ▴ 90
6
votes
14
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7.2k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 10.9 years ago by 53k • written 10.9 years ago by • 0
0
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2
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1.9k
views
Ensembl Fungi GFF3 with GenomicFeatures : makeTranscriptDbFromGFF
genomicfeatures
updated 10.9 years ago by ★ 7.2k • written 10.9 years ago by ▴ 90
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0
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1.2k
views
makeTranscriptDbFromGFF errors when loading bacterial genes from gff
genomicfeatures rnaseq
10.9 years ago agd27 • 0
3
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2
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3.7k
views
Cannot install GenomicFeatures package (related to RSQLite version)
biocinstaller genomicfeatures rsqlite
updated 10.9 years ago by ★ 8.2k • written 10.9 years ago by • 0
1
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2
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3.1k
views
GenomicFeatures::getPromoterSeq error when selecting all promoters sequences (in mice)
GenomicFeatures getPromoterSeq
updated 11.0 years ago by 68k • written 11.0 years ago by ▴ 120
1
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2
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1.6k
views
Missing values when extracting 5'UTR using GenomicFeatures?
GenomicFeatures 5'UTR
updated 11.0 years ago by 16k • written 11.0 years ago by ▴ 10
1
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4
replies
1.3k
views
Documentation for FeatureDB class?
FeatureDB GenomicFeatures
updated 11.1 years ago by 68k • written 11.1 years ago by ★ 3.8k
0
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3
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2.5k
views
Error running makeTranscriptDbFromGFF in GenomicFeatures
Genetics TranscriptDb GenomicFeatures
updated 11.2 years ago by ★ 11k • written 11.2 years ago by ▴ 270
0
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0
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2.6k
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Plot exon number per gene and transcript lengths
Genetics TranscriptDb GenomicFeatures
11.2 years ago Jon Bråte ▴ 270
0
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1
reply
2.2k
views
Protein position to genomic location
GenomicFeatures GenomicFeatures
updated 11.2 years ago by 1.6k • written 11.2 years ago by ★ 13k
0
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10
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3.5k
views
GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer RNAseqData GenomicFeatures Cancer RNAseqData GenomicFeatures
updated 11.3 years ago by ▴ 320 • written 11.4 years ago by ★ 6.8k
0
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5
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2.6k
views
makeTranscriptDbFromGFF Error for UCSC GTF File
GenomicFeatures GenomicFeatures
updated 11.3 years ago by ★ 7.2k • written 11.3 years ago by ★ 1.6k
0
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0
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1.4k
views
GenomicAlignments - Speeding up readGAlignmentPairs()
GenomicFeatures GenomicFeatures
11.4 years ago Fong Chun Chan ▴ 320
8
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3
replies
6.9k
views
Renaming the seqlevels in a transcript database from GenomicFeatures
GenomicFeatures GenomicFeatures
updated 11.4 years ago by ▴ 390 • written 11.4 years ago by ▴ 320
0
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2
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2.7k
views
Genomic Features - makeTranscriptDbFromGFF()
Organism TranscriptDb GenomicFeatures Organism TranscriptDb GenomicFeatures
updated 11.4 years ago by ★ 7.2k • written 11.4 years ago by ★ 13k
0
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0
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969
views
GenomicFeatures::makeTranscriptDbFromUCSC broken?
GenomicFeatures GenomicFeatures
11.5 years ago Michael Lawrence ★ 11k
0
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1
reply
1.3k
views
GenomicFeatures support for UCSC Microbial Genome Browser
GenomicFeatures GenomicFeatures
updated 11.8 years ago by 16k • written 11.8 years ago by ★ 13k
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2
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1.6k
views
Where can I download/install old packages like 'org.Rn.eg.db' based on rn4?
Annotation GO BSgenome TranscriptDb BSgenome GenomicFeatures Annotation GO BSgenome
updated 11.8 years ago by 16k • written 11.8 years ago by ▴ 60
0
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4
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1.8k
views
retrieving annotation
Annotation biomaRt GenomicFeatures Annotation biomaRt GenomicFeatures
updated 12.0 years ago by 16k • written 12.0 years ago by ▴ 110
0
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4
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2.4k
views
bug in GenomicRanges gaps?
GenomicFeatures GenomicRanges GenomicFeatures GenomicRanges
updated 12.2 years ago by ★ 1.6k • written 12.2 years ago by ▴ 220
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3
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2.1k
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makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
TranscriptDb convert GenomicFeatures TranscriptDb convert GenomicFeatures
12.2 years ago Sarah Pohl ▴ 30
0
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5
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2.7k
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problem generating Chinese hamster txdb from GFF file
GO GenomicFeatures GO GenomicFeatures
updated 3 months ago by • 0 • written 12.2 years ago by ★ 4.1k
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2
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1.4k
views
*Ranges paper published
Infrastructure IRanges GenomicFeatures GenomicRanges Infrastructure IRanges GenomicFeatures
updated 12.2 years ago by ★ 4.2k • written 12.2 years ago by ★ 11k
0
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4
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1.7k
views
IRanges::unlist in package
rtracklayer IRanges GenomicFeatures Rsamtools rtracklayer IRanges GenomicFeatures Rsamtools
updated 12.2 years ago by 68k • written 12.2 years ago by ▴ 220
0
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5
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4.6k
views
Failed to obtain \'hguid\' cookie for UCSC browser session
GenomicFeatures GenomicFeatures
updated 12.3 years ago by ★ 8.2k • written 12.3 years ago by ★ 13k
0
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2
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1.1k
views
using a gtf file to map reads
GO GenomicFeatures DEXSeq GO GenomicFeatures DEXSeq
updated 12.4 years ago by ★ 1.9k • written 12.4 years ago by ★ 6.8k
0
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3
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2.9k
views
DEXSeq Issue
Alignment Annotation GO Homo sapiens TranscriptDb PROcess GenomicFeatures DEXSeq Alignment
updated 12.4 years ago by 43k • written 12.4 years ago by ▴ 150
0
votes
1
reply
1.6k
views
problem installing GenomicFeatures
GenomicFeatures BiocInstaller GenomicFeatures BiocInstaller
updated 12.5 years ago by ★ 13k • written 12.5 years ago by ★ 13k
0
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1
reply
1.7k
views
makeTranscriptDbFromBiomart - chrominfo failure
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 12.6 years ago by ★ 7.2k • written 12.6 years ago by ▴ 360
0
votes
6
replies
2.0k
views
What happened to GenomicFeatures::spliceGraph?
GenomicFeatures GenomicFeatures
updated 12.7 years ago by ★ 4.2k • written 12.7 years ago by ★ 7.9k
0
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0
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989
views
Extract Exon Features from GenomicFeatures Leads to Inconsistent Pairing of Gene and Exon IDs
Cancer GenomicFeatures Cancer GenomicFeatures
12.7 years ago Hervé Pagès 16k
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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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