Showing : GenomicFeatures • reset
4
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2
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1.7k
views
distinguish DataSource from Provider and ProviderVersion in makeTxDbPackage
genomicfeatures txdb maketxdbfromgff metadata
updated 9.5 years ago by ★ 6.8k • written 9.5 years ago by ▴ 80
4
votes
2
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1.5k
views
Get internal exons using GenomicFeatures
genomicfeatures granges
updated 9.5 years ago by ★ 11k • written 9.5 years ago by ▴ 10
0
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5
replies
2.2k
views
makeTxDbFromGFF returns empty object
genomicfeatures txdb maketxdbfromgff
9.5 years ago TimothéeFlutre ▴ 80
0
votes
2
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1.3k
views
GenomicFeatures coordinates UCSC
genomicfeatures txdb.hsapiens.ucsc.hg19.knowngene
9.6 years ago • updated 9.5 years ago ribioinfo ▴ 100
0
votes
2
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1.9k
views
mapFromTranscripts strand problem
mapFromTranscripts genomicfeatures
updated 9.5 years ago by ★ 6.8k • written 9.6 years ago by • 0
0
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0
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1.3k
views
extractUpstreamSeqs with custom genome, no gene_id shown
genomicranges txdb genomicfeatures featureextraction
updated 9.6 years ago by 25k • written 9.6 years ago by ▴ 30
1
vote
4
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1.6k
views
calculate total transcript length from DisjointExons output (Genomic Ranges Object)
genomicfeatures non overlapping exons genomicranges granges
updated 9.6 years ago by ★ 11k • written 9.6 years ago by ▴ 30
8
votes
24
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5.0k
views
GenomicFeatures: Select exons by transcript. Any faster option than exonsBy?
GenomicFeatures
updated 9.6 years ago by 25k • written 9.6 years ago by ▴ 90
1
vote
3
replies
1.2k
views
Extract information from GenomicRanges
genomicranges genomicfeatures
9.6 years ago ribioinfo ▴ 100
0
votes
2
replies
1.4k
views
Error when trying to load a gff3 with GenomicFeatures
genomicfeatures
updated 9.6 years ago by ★ 6.6k • written 9.6 years ago by • 0
0
votes
1
reply
1.4k
views
Error message in makeTxDbFromGFF()
iranges genomicfeatures
updated 9.7 years ago by 43k • written 9.7 years ago by • 0
0
votes
1
reply
1.6k
views
How to find index position of desired feature_by in TxDb granges?
granges txdb genomicfeatures
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 50
4
votes
2
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2.0k
views
Restricting seqlevels to chr1-chr22, chrX, chrY in TxDb from UCSC returns more genes than without restriction
GenomicFeatures
updated 9.7 years ago by 25k • written 9.7 years ago by ▴ 10
4
votes
5
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1.6k
views
Write multiple UTRs for a gene to a fasta file
genomicranges genomicfeatures
updated 9.8 years ago by ★ 11k • written 9.8 years ago by ▴ 90
1
vote
4
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2.0k
views
GenomicFeatures makeTranscriptDbFromBiomart 'chrominfo' data frame ... FAILED!
genomicfeatures
updated 9.8 years ago by 16k • written 9.8 years ago by ▴ 200
2
votes
5
replies
2.6k
views
TxDb.Hsapiens.UCSC.hg19.knownGene Exons that are not part of any gene
TxDb.Hsapiens.UCSC.hg19.knownGene genomicfeatures annotation
9.8 years ago Aliaksei Holik ▴ 350
2
votes
1
reply
1.1k
views
Problem while installing genomicfeatures package.
genomicfeatures
9.8 years ago vinod.acear ▴ 50
0
votes
8
replies
5.9k
views
error making txdb object from gtf file
genomicfeatures
updated 9.8 years ago by ★ 2.1k • written 9.8 years ago by ▴ 20
9
votes
21
replies
13k
views
annotate GRanges with upstream or downstream nearest gene
GRange genomicranges genomicfeatures
updated 9.8 years ago by ★ 1.3k • written 9.8 years ago by ▴ 200
2
votes
10
replies
3.0k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 9.9 years ago by ★ 11k • written 9.9 years ago by ▴ 10
0
votes
1
reply
1.8k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 3.9 years ago by • 0 • written 9.9 years ago by ▴ 10
4
votes
5
replies
4.0k
views
How to find the amino acid codon corresponding to a translated genomic position
genomicranges genomicfeatures translation
updated 21 months ago by ▴ 10 • written 9.9 years ago by ▴ 10
0
votes
7
replies
2.4k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures maketxdbfromgff tx_type gtf
updated 9.9 years ago by 16k • written 9.9 years ago by • 0
0
votes
0
replies
1.4k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures maketxdbfromgff tx_type gtf
9.9 years ago Karolin Wiedemann • 0
0
votes
4
replies
2.5k
views
Error running makeTxDbFromGFF
genomicfeatures
updated 10.0 years ago by ▴ 180 • written 10.0 years ago by • 0
0
votes
7
replies
2.9k
views
makeTxDbFromGFF yields an empty TxDb
annotation maketxdbfromgff genomicfeatures
10.0 years ago José Luis Lavín ▴ 10
1
vote
5
replies
2.3k
views
'version' is missing error when running makeTxDbPackageFromUCSC
Cancer TranscriptDb IRanges GenomicFeatures Cancer TranscriptDb IRanges GenomicFeatures
updated 10.0 years ago by ▴ 10 • written 12.2 years ago by 16k
4
votes
7
replies
3.4k
views
How to get Genomic feature in txdb format from biomart for sacCer2 (EF4) assembly?
makeTxDbFromBiomart genomicfeatures txdb biomart
updated 10.0 years ago by 68k • written 10.0 years ago by ▴ 50
3
votes
7
replies
3.5k
views
Failed to set session genome to ...
genomicfeatures makeTxDbFromUCSC
updated 10.0 years ago by ★ 11k • written 10.5 years ago by ▴ 100
1
vote
2
replies
2.4k
views
Problem when installing GenomicFeatures on GNU/Linux server
edger genomicfeatures
updated 10.0 years ago by 68k • written 10.0 years ago by ▴ 40
1
vote
1
reply
2.2k
views
GenomicFeatures, makeTxDbFromGFF: select only certain types from a gtf file
genomicfeatures
updated 10.1 years ago by 16k • written 10.1 years ago by ▴ 50
0
votes
3
replies
1.8k
views
possible conflict between renameSeqLevels (TxDb) and isActiveSeq (TxDb)
bug txdb genomicfeatures
10.2 years ago • updated 10.1 years ago Robert K. Bradley ▴ 40
0
votes
2
replies
1.3k
views
renamed seqlevels (TxDb) don't persist through a save-load cycle
GenomicFeatures TxDb
10.2 years ago • updated 10.1 years ago Robert K. Bradley ▴ 40
2
votes
12
replies
2.4k
views
remove set number of nucleotides from each gene's cds region in GRangesList
genomicranges genomicfeatures
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ▴ 90
0
votes
1
reply
2.0k
views
BugReport: genomicFeatures - makeTxDbFromGFF does not work
GenomicFeatures
10.2 years ago aldobiasova • 0
3
votes
2
replies
1.6k
views
gene model generation support?
granges gene models GenomicFeatures
10.5 years ago • updated 10.2 years ago Vincent J. Carey, Jr. 6.7k
0
votes
1
reply
2.1k
views
makeTxdbfromUCSC Warning message
MakeTXDCfromUCSC GenomicFeatures warning
updated 10.2 years ago by ★ 7.2k • written 10.2 years ago by ▴ 10
0
votes
6
replies
2.5k
views
problem using makeTxDbFromGFF and exonsBy() functions
annotation genomicfeatures
updated 10.3 years ago by ★ 1.3k • written 10.3 years ago by ▴ 10
0
votes
1
reply
1.9k
views
Getting data on the out-of-frame transcripts
annotate sequencing genomicfeatures
updated 10.3 years ago by 16k • written 10.3 years ago by • 0
0
votes
4
replies
1.1k
views
problem using makeTranscriptDbFromGFF parsing cyno GFF
genomicfeatures
updated 10.3 years ago by 16k • written 10.3 years ago by • 0
0
votes
6
replies
4.0k
views
RNA-seq analysis with R/BioC: alignment and read counts
drosophila melanogaster quasR genomicfeatures genomicranges alignment
updated 10.3 years ago by 16k • written 10.3 years ago by ▴ 70
0
votes
1
reply
882
views
danRer10 BSgenome file
genomicfeatures
updated 10.3 years ago by 68k • written 10.3 years ago by • 0
1
vote
3
replies
1.8k
views
GenomicFeatures error: rsqlite_query_send: could not execute1: database or disk is full
genomicfeatures rnaseq deseq2
10.3 years ago Xiaokuan Wei ▴ 230
0
votes
3
replies
4.1k
views
‘GenomicFeatures’ is not available (for R version 3.2.0)
genomicfeatures
updated 10.4 years ago by ▴ 10 • written 10.4 years ago by • 0
5
votes
2
replies
3.8k
views
Saving/loading TxDb objects
genomicfeatures
updated 10.4 years ago by 25k • written 10.4 years ago by 68k
4
votes
2
replies
1.7k
views
Count reads with package "bamsignals" from a female bam file (no chrY)
bamsignals genomicfeatures
updated 10.4 years ago by ▴ 20 • written 10.4 years ago by ▴ 10
0
votes
1
reply
1.6k
views
Extract exon features from overlapping genes
GenomicFeatures exons
updated 10.4 years ago by 16k • written 10.4 years ago by • 0
2
votes
5
replies
1.8k
views
mapToTranscripts stranded behavior
genomicfeatures
updated 10.4 years ago by ★ 6.8k • written 10.5 years ago by 43k
8
votes
16
replies
3.8k
views
Setting package name in makeTxDbPackage
genomicfeatures txdb
updated 10.5 years ago by ★ 7.2k • written 10.5 years ago by ▴ 760
2
votes
2
replies
1.7k
views
Setting genome information on a TxDb object
genomicfeatures txdb
updated 10.5 years ago by 16k • written 10.5 years ago by ▴ 760
291 results • Page 4 of 6
Recent ...
Replies
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
Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k
we can investigate this issue. thank you for bringing it to our attention
Comment: deseq2 filter the low counts by Michael Love 43k
> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…
Comment: deseq2 filter the low counts by empty_mt • 0
Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …
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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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