Showing : transcriptdb • reset
2
votes
30
replies
4.4k
views
ggbio 1.12.0 autoplot() with txdb example is broken
TranscriptDb TranscriptDb
updated 10.0 years ago by ▴ 490 • written 10.1 years ago by ★ 1.0k
0
votes
3
replies
1.5k
views
TranscriptDb object to RangedData for ChIPpeakAnno
Annotation GO AnnotationData Organism BSgenome TranscriptDb convert BSgenome ChIPpeakAnno
10.8 years ago Alan Smith ▴ 150
1
vote
5
replies
1.9k
views
'version' is missing error when running makeTxDbPackageFromUCSC
Cancer TranscriptDb IRanges GenomicFeatures Cancer TranscriptDb IRanges GenomicFeatures
updated 8.5 years ago by ▴ 10 • written 10.7 years ago by 16k
0
votes
3
replies
1.4k
views
predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 11.6 years ago by 16k • written 11.6 years ago by ▴ 100
0
votes
3
replies
1.7k
views
makeTranscriptDbFromGFF fails on NCBI Bacteria genomes
TranscriptDb convert GenomicFeatures TranscriptDb convert GenomicFeatures
10.7 years ago Sarah Pohl ▴ 30
0
votes
2
replies
956
views
GenomicFeatures: Unable to save TranscriptDb object
TranscriptDb TranscriptDb
updated 13.1 years ago by 16k • written 13.1 years ago by ▴ 20
0
votes
2
replies
2.4k
views
Genomic Features - makeTranscriptDbFromGFF()
Organism TranscriptDb GenomicFeatures Organism TranscriptDb GenomicFeatures
updated 9.9 years ago by ★ 7.2k • written 9.9 years ago by ★ 13k
0
votes
10
replies
2.8k
views
MakeTranscriptDbFromGFF
Annotation TranscriptDb Annotation TranscriptDb
updated 11.0 years ago by ★ 7.2k • written 11.0 years ago by ▴ 340
0
votes
3
replies
893
views
Question about TranscriptDb and makeTranscriptDb method
TranscriptDb TranscriptDb
updated 13.4 years ago by 16k • written 13.4 years ago by ▴ 60
0
votes
3
replies
1.1k
views
Is there a place to download GenomicFeatures' sqlite from ensembl.
TranscriptDb TranscriptDb
updated 13.4 years ago by ★ 11k • written 13.4 years ago by ▴ 970
0
votes
2
replies
814
views
Is there a place to download GenomicFeatures'
TranscriptDb TranscriptDb
updated 13.4 years ago by ★ 13k • written 13.4 years ago by ▴ 20
0
votes
3
replies
1.1k
views
RE : RE : RE : maping SNPs
GO TranscriptDb GO TranscriptDb
updated 13.3 years ago by 16k • written 13.3 years ago by ▴ 450
0
votes
1
reply
838
views
In the TranscriptDb object, where do the Entrez Gene IDs come from ?
TranscriptDb TranscriptDb
updated 13.3 years ago by ★ 7.2k • written 13.3 years ago by ▴ 10
0
votes
2
replies
1.6k
views
extending GenomicFeatures to makeTranscriptDbFrom other sources (i.e. GFF3)
TranscriptDb biomaRt TranscriptDb biomaRt
updated 13.2 years ago by ★ 7.2k • written 13.2 years ago by ★ 1.6k
0
votes
1
reply
1.8k
views
TranscriptDB object
TranscriptDb TranscriptDb
updated 12.8 years ago by 16k • written 12.8 years ago by ★ 1.5k
0
votes
4
replies
1.5k
views
GenomicFeatures makeTranscriptDbFromBiomart failure
TranscriptDb biomaRt TranscriptDb biomaRt
updated 12.5 years ago by ★ 11k • written 12.5 years ago by ▴ 270
0
votes
1
reply
685
views
subsetting transcriptDb
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 12.3 years ago by ★ 7.2k • written 12.3 years ago by ▴ 360
0
votes
3
replies
1.8k
views
RE : maping SNPs
SNP Annotation Cancer SNPlocs TranscriptDb GenomicFeatures GenomicRanges SNP Annotation
updated 12.3 years ago by 16k • written 12.3 years ago by ▴ 450
0
votes
18
replies
1.8k
views
Create transcriptDb using gff3 files? - library GenomicFeatures and rtracklayer
TranscriptDb TranscriptDb
updated 12.1 years ago by ★ 13k • written 12.1 years ago by ▴ 230
1
vote
2
replies
1.3k
views
load a TranscriptDb object in another R session?
TranscriptDb TranscriptDb
updated 12.1 years ago by ★ 1.6k • written 12.1 years ago by ▴ 230
0
votes
1
reply
1.1k
views
VariantAnnotation locateVariants - meaning of precedesID and followsID
BSgenome TranscriptDb BSgenome GenomicFeatures BSgenome TranscriptDb BSgenome
updated 12.1 years ago by ★ 6.8k • written 12.1 years ago by ▴ 80
0
votes
2
replies
1.5k
views
RE : RE : maping SNPs
SNP SNPlocs TranscriptDb IRanges GenomicFeatures SNP SNPlocs TranscriptDb IRanges
updated 13.4 years ago by ★ 6.8k • written 13.4 years ago by ▴ 450
0
votes
1
reply
1.3k
views
Building a TranscriptDb object from a lncRNA gft file
TranscriptDb TranscriptDb
updated 11.2 years ago by ★ 7.2k • written 11.2 years ago by ▴ 320
0
votes
3
replies
2.4k
views
DEXSeq Issue
Alignment Annotation GO Homo sapiens TranscriptDb PROcess GenomicFeatures DEXSeq Alignment
updated 11.0 years ago by 42k • written 11.0 years ago by ▴ 150
0
votes
1
reply
1.4k
views
FW: Overlay Gene Expression on SNP (copy number) data
SNP Coverage Network Cancer TranscriptDb IRanges RCytoscape ggbio Gviz SNP Coverage
updated 12.1 years ago by ★ 4.2k • written 12.1 years ago by ▴ 370
0
votes
2
replies
1.1k
views
building a refseq-based transcriptDb: warnings of interest?
TranscriptDb TranscriptDb
updated 13.8 years ago by 16k • written 13.8 years ago by 6.7k
0
votes
1
reply
960
views
TranscriptDb and genomicranges questions
Cancer TranscriptDb Category IRanges GenomicRanges Cancer TranscriptDb Category IRanges
13.8 years ago Hervé Pagès 16k
0
votes
4
replies
1.6k
views
getting gene ranges from a TranscriptDb (GenomicFeatures package)
GO TranscriptDb GO TranscriptDb
updated 13.7 years ago by 21k • written 13.7 years ago by ▴ 210
0
votes
2
replies
915
views
IRanges, GenomicRanges, GenomicFeatures?
Coverage Annotation TranscriptDb convert GenomicFeatures Coverage Annotation TranscriptDb
updated 13.5 years ago by ★ 13k • written 13.5 years ago by ▴ 60
0
votes
3
replies
3.4k
views
Working with ensembl 73 & BSGenome
Annotation BSgenome TranscriptDb biomaRt BSgenome Annotation BSgenome TranscriptDb biomaRt
updated 10.5 years ago by 16k • written 10.5 years ago by ★ 13k
0
votes
2
replies
1.7k
views
autoplot transcriptDb error with some regions
TranscriptDb biovizBase ggbio TranscriptDb biovizBase ggbio
updated 10.5 years ago by ▴ 490 • written 10.5 years ago by ★ 1.6k
0
votes
3
replies
1.9k
views
autoplot() error on a GRanges object in ggbio 1.10.8
Annotation TranscriptDb Annotation TranscriptDb
updated 10.5 years ago by ▴ 490 • written 10.5 years ago by ★ 1.0k
0
votes
2
replies
1.5k
views
tracks() and plotIdeogram() with non desired results in ggbio 1.10.9
TranscriptDb ideogram TranscriptDb ideogram
updated 10.5 years ago by ▴ 490 • written 10.5 years ago by ★ 1.0k
0
votes
1
reply
1.2k
views
tracks() and plotIdeogram() with non desired results in ggbio 1.10.9
TranscriptDb ideogram ggbio TranscriptDb ideogram ggbio
updated 10.4 years ago by ★ 1.0k • written 10.4 years ago by ▴ 490
0
votes
2
replies
1.2k
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 10.4 years ago by 16k • written 10.4 years ago by ▴ 60
0
votes
1
reply
2.1k
views
makeTranscriptDbFromUCSC
TranscriptDb TranscriptDb
10.3 years ago Georg Otto ▴ 120
0
votes
1
reply
1.5k
views
Error in combining GRanges objects into GRangesList object
TranscriptDb TranscriptDb
updated 10.2 years ago by ★ 11k • written 10.2 years ago by ▴ 10
0
votes
4
replies
1.4k
views
Extracting strand information from GenomicFeatures transcript db objects
TranscriptDb biomaRt TranscriptDb biomaRt
updated 10.2 years ago by 16k • written 10.2 years ago by ▴ 100
0
votes
2
replies
2.0k
views
UCSC data anomaly in 50638 transcript(s): the cds cumulative length is
Genetics GO Regression Cancer TranscriptDb Genetics GO Regression Cancer TranscriptDb
updated 10.0 years ago by ▴ 570 • written 10.0 years ago by 16k
6
votes
2
replies
5.3k
views
Get sequences for GRCh38 genome based on TxDb object locations
bsgenome genomeinfodb transcriptdb
updated 9.4 years ago by 16k • written 9.4 years ago by ▴ 760
0
votes
1
reply
1.0k
views
BugReports: bug with runValue (strand (GRangesList))
transcriptdb
updated 9.5 years ago by 16k • written 9.5 years ago by ▴ 40
0
votes
1
reply
696
views
creating transcriptDB from gff3 files
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 11.8 years ago by ★ 6.8k • written 11.8 years ago by ▴ 210
0
votes
4
replies
2.1k
views
predictCoding() return empty Granges
Annotation Cancer Arabidopsis thaliana BSgenome SNPlocs TranscriptDb BSgenome Annotation
updated 11.6 years ago by 16k • written 11.6 years ago by ▴ 100
0
votes
2
replies
2.0k
views
Extracting strand information from GenomicFeatures transcript db objects
TranscriptDb biomaRt TranscriptDb biomaRt
updated 11.3 years ago by ★ 6.8k • written 11.3 years ago by ▴ 100
0
votes
1
reply
1.4k
views
makeTranscriptDbFromBiomart - chrominfo failure
TranscriptDb GenomicFeatures TranscriptDb GenomicFeatures
updated 11.2 years ago by ★ 7.2k • written 11.2 years ago by ▴ 360
0
votes
3
replies
1.7k
views
retrieving external Gene IDs from TranscriptDB Object
Yeast TranscriptDb Yeast TranscriptDb
updated 11.0 years ago by ▴ 340 • written 11.0 years ago by ▴ 360
0
votes
4
replies
1.9k
views
makeTranscriptDbFromGFF for Unstranded Transcripts
TranscriptDb TranscriptDb
updated 11.0 years ago by 16k • written 11.0 years ago by ★ 1.5k
0
votes
1
reply
1.4k
views
Question about MEDIPS extend parameter : RE: Success: RE: Seed file error: RE: BioStrings for current R: RE: BSgenomeForge seed file - seqnames field
Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome MEDIPS
updated 10.4 years ago by ▴ 240 • written 10.4 years ago by 16k
0
votes
2
replies
1.2k
views
'version' is missing error when running makeTxDbPackageFromUCSC
TranscriptDb IRanges TranscriptDb IRanges
updated 10.7 years ago by ★ 8.2k • written 10.7 years ago by ▴ 40
0
votes
3
replies
2.1k
views
Error running makeTranscriptDbFromGFF in GenomicFeatures
Genetics TranscriptDb GenomicFeatures
updated 9.7 years ago by ★ 11k • written 9.7 years ago by ▴ 250
50 results • Page 1 of 1
Recent ...
Replies
Comment: More regions in union when increasing DBA$config$mergeOverlap by Ziliang • 0
I am so confused and frustrated learning to use this software. Isn't how you merge the peaksets one of the most important steps for the com…
Answer: SingleR Label.Ont by Denis • 0
[Jackpot City Casino][1] is the perfect option when looking for an online casino in Canada for an exciting vacation and huge winnings that …
Comment: deseq2 results by sajadahmad41454 • 0
thank you so much and sorry for bothering you again and again, it is urgent because it is my project deadline. i have removed that sample a…
Comment: deseq2 results by swbarnes2 ★ 1.4k
Ask the people who made the libraires if there was anything unusual in the QC of the outlier sample. Try to figure out what biologically …
Comment: Can't post a question containing code? by NATASHA • 0
did you find a solution? I´m having the same problem
Votes
A: AIC-like measure for DESeq2
Comment: Extremely small p-values using Limma for proteomic data
Comment: Log-cpm values from limma
Comment: Log-cpm values from limma
Comment: deseq2 results
Awards • All
Popular Question to maria.soler • 0
Popular Question to Pietro ▴ 40
Popular Question to neilzhao ▴ 30
Popular Question to ATpoint ★ 4.1k
Teacher to Michael Love 42k
Locations • All
United States, 2 minutes ago
France, 18 minutes ago
UPF, Barcelona, Spain, 21 minutes ago
The city by the bay, 1 hour ago
EMBL Heidelberg, 2 hours ago
Traffic: 542 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6