Showing : genomicfeatures • reset
8
votes
24
replies
4.4k
views
GenomicFeatures: Select exons by transcript. Any faster option than exonsBy?
GenomicFeatures
updated 9.0 years ago by 25k • written 9.0 years ago by ▴ 90
1
vote
23
replies
3.1k
views
Distance calculation for variants in intergenic regions
locatevariants variantannotation genomicfeatures
updated 8.4 years ago by ★ 11k • written 8.4 years ago by • 0
9
votes
21
replies
12k
views
annotate GRanges with upstream or downstream nearest gene
GRange genomicranges genomicfeatures
updated 9.2 years ago by ★ 1.3k • written 9.2 years ago by ▴ 200
8
votes
20
replies
6.7k
views
Issue when import genomic features from the file :Error in parseURI("") : cannot parse URI (issue resolved)
genomicfeatures xml libxml2
8.1 years ago • updated 8.0 years ago JunLVI ▴ 40
0
votes
18
replies
4.8k
views
Indexing FASTA file using RSamtools
Rsamtools GenomicFeatures
3.1 years ago rbenel ▴ 40
8
votes
16
replies
3.3k
views
Setting package name in makeTxDbPackage
genomicfeatures txdb
updated 9.8 years ago by ★ 7.2k • written 9.9 years ago by ▴ 760
2
votes
16
replies
4.7k
views
TxDb annotations for human chrM
GenomicFeatures TxDb.Hsapiens.UCSC.hg19.knownGene annotation
10.2 years ago • updated 10.1 years ago Robert Castelo ★ 3.4k
6
votes
14
replies
6.7k
views
GenomicAlignments is too slow with summarizeOverlaps
genomicalignments RNASeq genomicfeatures summarizeoverlaps
updated 10.2 years ago by 52k • written 10.2 years ago by • 0
1
vote
14
replies
3.8k
views
DEXSeq - dexseq_count.py issue
dexseq dexseq_count genomicfeatures
updated 6.9 years ago by • 0 • written 7.0 years ago by • 0
3
votes
13
replies
3.0k
views
IRanges error from derfinder analyzeChr with custom TxDb?
derfinder genomicfeatures genomicranges
updated 7.6 years ago by ★ 1.1k • written 7.6 years ago by ▴ 20
2
votes
13
replies
2.9k
views
makeTranscriptDbFromBiomart failure from Data Anomaly
biomart genomicfeatures
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 80
3
votes
13
replies
3.7k
views
Getting errors with makeTxDbFromBiomart
genomicfeatures biomart maketxdbfrombiomart
updated 8.2 years ago by ▴ 800 • written 8.2 years ago by ▴ 10
0
votes
13
replies
3.3k
views
multiple hits with countOverlaps function
Sequencing GenomicFeatures Sequencing GenomicFeatures
13.9 years ago Wei Shi ★ 3.6k
2
votes
12
replies
2.1k
views
remove set number of nucleotides from each gene's cds region in GRangesList
genomicranges genomicfeatures
updated 9.6 years ago by ★ 11k • written 9.6 years ago by ▴ 90
8
votes
12
replies
6.4k
views
Intergenic coordinates with Genomic Feaures
genomicranges genomicfeatures iranges
updated 2.7 years ago by • 0 • written 10.0 years ago by ▴ 20
0
votes
10
replies
3.2k
views
GenomicAlignments - Speeding up readGAlignmentPairs()
Cancer RNAseqData GenomicFeatures Cancer RNAseqData GenomicFeatures
updated 10.7 years ago by ▴ 320 • written 10.7 years ago by ★ 6.8k
3
votes
10
replies
4.3k
views
CDS phase information missing from GenomicFeatures
GenomicFeatures phase gene models GFF
updated 7.4 years ago by 16k • written 7.5 years ago by ▴ 10
3
votes
10
replies
5.2k
views
Getting a list of all tRNA encoding genes for an organism?
trna ncrna genomicfeatures featuredb biomart
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 180
1
vote
10
replies
4.0k
views
Issue creating a genomic state object in derfinder from an Ensembl GTF file
derfinder genomicfeatures
8.1 years ago Leonardo Collado Torres ★ 1.1k
2
votes
10
replies
2.7k
views
How to find the amino acid codons corresponding to a subset of a range of genomic positions
genomicfeatures genomicranges cds overlap
updated 9.3 years ago by ★ 11k • written 9.3 years ago by ▴ 10
0
votes
9
replies
2.2k
views
Mapping microarray probes to the genome using findOverlaps
Microarray Alignment Annotation zebrafish probe Biostrings GenomicFeatures Microarray
updated 14.1 years ago by 21k • written 14.1 years ago by 16k
5
votes
9
replies
2.1k
views
Questions regarding failing tximeta import for swish
swish fishpond GenomicFeatures tximeta
updated 2.6 years ago by 43k • written 3.0 years ago by • 0
4
votes
9
replies
2.2k
views
Issues with seqlevelsStyle when making custom txdb objects for genomes/annotations from ToxoDB
txdbmaker GenomeInfoDb GenomicFeatures Biostrings gDNAx
updated 8 weeks ago by ★ 3.4k • written 3 months ago by ▴ 20
0
votes
9
replies
4.2k
views
genomicfeatures rsqlite database or disk is full
genomicfeatures
updated 10.0 years ago by ★ 7.2k • written 10.0 years ago by ▴ 90
1
vote
8
replies
3.1k
views
Trying to map nucleotide position from a transcript to genomic location
genomicfeatures mapfromtranscripts mirna
updated 6.5 years ago by ★ 6.8k • written 6.5 years ago by ▴ 20
4
votes
8
replies
2.4k
views
TxDB.Hsapiens.UCSC.hg38.knownGene with locateVariants() identifying SNPs from various chromosome being part of the same gene
MetID TxDB.Hsapiens.UCSC.hg38.knownGene locateVariants GenomicFeatures VariantAnnotation
2.0 years ago davidhillis • 0
1
vote
8
replies
2.7k
views
makeTxDbFromUCSC("hg38", "refGene") gives "not supported" error
GenomicFeatures
updated 8.0 years ago by 16k • written 8.0 years ago by ▴ 10
0
votes
8
replies
5.5k
views
error making txdb object from gtf file
genomicfeatures
updated 9.2 years ago by ★ 2.1k • written 9.2 years ago by ▴ 20
1
vote
8
replies
3.7k
views
GenomicFeatures package ERROR
software error genomicfeatures
updated 7.8 years ago by ★ 11k • written 9.3 years ago by • 0
0
votes
8
replies
2.2k
views
exonsBy does not order exons by ascending rank, is it a bug or outdated documentation?
GenomicFeatures GenomicAlignment GenomicAlignments exonBy coverageByTranscript
updated 5.4 years ago by 16k • written 5.4 years ago by ▴ 90
0
votes
8
replies
2.5k
views
makeTranscriptDbFromGFF Unexpected transcript duplicates
genomicfeatures
10.1 years ago Miss Agnieszka Aleksandra Golicz ▴ 40
3
votes
7
replies
2.3k
views
Add up RLEs that are in lists?
RLE GenomicFeatures rnaseq
updated 10.0 years ago by 16k • written 10.0 years ago by ▴ 30
0
votes
7
replies
2.0k
views
Mapping genomic coordinates to transcript coordinates? (revived)
Biostrings GenomicFeatures Biostrings GenomicFeatures
updated 14.0 years ago by ★ 11k • written 14.1 years ago by 16k
0
votes
7
replies
2.2k
views
Get wrong tx_type when using GenomicFeatures::makeTxDbFromGTF
genomicfeatures maketxdbfromgff tx_type gtf
updated 9.3 years ago by 16k • written 9.3 years ago by • 0
1
vote
7
replies
6.6k
views
Existence of a makeTxDbFromGFF function in GenomicFeatures package?
genomicfeatures
9.9 years ago pterry • 0
2
votes
7
replies
5.5k
views
Extend GRanges start/end
Genetics GenomicFeatures Genetics GenomicFeatures
updated 12.4 years ago by ★ 11k • written 12.4 years ago by ▴ 510
6
votes
7
replies
2.9k
views
makeTxDbFromUCSC fails to download refLink table
genomicfeatures maketxdbfromucsc refseq
updated 8.7 years ago by 16k • written 8.7 years ago by ▴ 10
4
votes
7
replies
3.1k
views
How to get Genomic feature in txdb format from biomart for sacCer2 (EF4) assembly?
makeTxDbFromBiomart genomicfeatures txdb biomart
updated 9.4 years ago by 68k • written 9.4 years ago by ▴ 50
0
votes
7
replies
2.7k
views
makeTxDbFromGFF yields an empty TxDb
annotation maketxdbfromgff genomicfeatures
9.4 years ago José Luis Lavín ▴ 10
0
votes
7
replies
1.4k
views
GenomicFeatures::makeTranscriptDbFromGTF?
Cancer GenomicFeatures Cancer GenomicFeatures
updated 13.1 years ago by ★ 11k • written 13.1 years ago by ★ 13k
2
votes
7
replies
1.6k
views
Peaks in coverageByTranscript {GenomicFeatures}
GenomicFeatures
updated 7.9 years ago by 16k • written 7.9 years ago by • 0
5
votes
7
replies
2.3k
views
Possible error in TxDb.Mmusculus.UCSC.mm10.ensGene_3.4.0?
txdb genomicfeatures
updated 8.0 years ago by 68k • written 8.0 years ago by ▴ 40
0
votes
7
replies
2.1k
views
Speeding up or replacing Loops to process Bam Reads
genomicranges reads genomicfeatures Bam
10.0 years ago gen ▴ 30
3
votes
7
replies
3.3k
views
Failed to set session genome to ...
genomicfeatures makeTxDbFromUCSC
updated 9.4 years ago by ★ 11k • written 9.9 years ago by ▴ 100
3
votes
7
replies
1.9k
views
GRanges/GFeatures: Retain all parent columns in cdsByOverlaps output
GRanges GenomicRanges GenomicFeatures cdsByOverlaps DiffBind
updated 4.6 years ago by 68k • written 4.6 years ago by ▴ 30
3
votes
6
replies
2.2k
views
cummeRbund installation fails
bioconductor cummerbund software error GenomicFeatures
updated 7.3 years ago by 25k • written 7.3 years ago by ▴ 30
5
votes
6
replies
4.1k
views
error in makeTxDbFromUCSC
genomicfeatures R bioconductor maketxdbfromucsc
updated 6.2 years ago by 16k • written 6.2 years ago by • 0
8
votes
6
replies
2.3k
views
Error when running "locateVariants" function in "VariantAnnotation" package
variantannotation tidyverse genomicfeatures
updated 7.5 years ago by 16k • written 7.6 years ago by ▴ 20
0
votes
6
replies
1.8k
views
What happened to GenomicFeatures::spliceGraph?
GenomicFeatures GenomicFeatures
updated 12.1 years ago by ★ 4.2k • written 12.1 years ago by ★ 7.9k
6
votes
6
replies
2.2k
views
GenomicFeatures makeTxDbFromBiomart fails with "unkown species" error
biomart maketxdbfrombiomart genomicfeatures
updated 8.1 years ago by 68k • written 8.1 years ago by ▴ 30
50 results • Page 1 of 1
Recent ...
Replies
Comment: DiffBind custom normalization factor by Abbie • 0
Hello! Thanks so much for adding dba.normalize and all the documentation in the manual! I'm hoping I can ask a follow-up question here. I…
Answer: CpGs with genomic positions greater than the chromosome size in EPICv2? by James W. MacDonald 68k
All of the annotation packages provided by Bioconductor are simply repackaging of existing data from one or more sources. In this case, the…
Comment: Using TPM from tximport of Salmon output for singscore by Kent • 0
Thank you for the suggestions Michael. Would you say that after filtering out the low count genes, `rlog(counts, blind = T)` is doing the s…
Comment: Using TPM from tximport of Salmon output for singscore by Michael Love 43k
For clustering generally we recommend `vst()` see the workflow for example. For working with individual samples, I can see how a scaling/t…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by Michael Love 43k
I'd recommend working with a local statistician or someone familiar with linear models in R. I have to reserve my time on the support site …
Votes
clusterProfiler-GO enrichment Error
A: Machine learning in R book
Data preparation and Machine learning on time course RNAseq data
Data preparation and Machine learning on time course RNAseq data
Answer: Use of org.Rn.eg.db with GRCr8 reference genome
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