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Ensembldb
•
reset
3
votes
4
replies
13k
views
converting ensembl transcript ID to ensemble gene: problem & missing values
biomart
error
ensembldb
6.2 years ago
Yuqia
• 0
9
votes
11
replies
5.8k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 7 weeks ago by
shepherl
3.9k • written 2.3 years ago by
jon.klonowski
▴ 40
7
votes
36
replies
5.6k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 28 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
3
votes
8
replies
4.4k
views
EnsemblDb: how to retrieve gene name / description?
EnsDb.Mmusculus.v79
ensembldb
annotation
updated 6.7 years ago by
Johannes Rainer
★ 2.0k • written 6.7 years ago by
Guido Hooiveld
★ 3.9k
0
votes
3
replies
4.3k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb
tximport
salmon
updated 6.0 years ago by
Johannes Rainer
★ 2.0k • written 6.0 years ago by
user31888
▴ 30
7
votes
6
replies
4.1k
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 6 months ago by
Marcel Ramos
690 • written 20 months ago by
Recep
▴ 20
7
votes
8
replies
3.7k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport
ensembldb
EnsDB.hsapiens.v86
updated 5.3 years ago by
Bioconductor Community
0 • written 5.5 years ago by
michaelschoeber
▴ 20
5
votes
9
replies
3.5k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb
ensembl release
rnaseq
salmon
tximport
6.2 years ago
emmak
▴ 20
5
votes
6
replies
3.4k
views
How to build and map to a "pre-mRNA" reference transcriptome for single nucleus RNA-seq data?
tximeta
ensembldb
single-cell
snRNA-seq
tximport
updated 4.6 years ago by
Robert Castelo
★ 3.3k • written 4.6 years ago by
Stephanie Hicks
▴ 80
5
votes
1
reply
3.3k
views
Tutorial:
Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread
rsubread
ensembldb
Tutorial
8.1 years ago
phil.chapman
▴ 150
6
votes
11
replies
3.2k
views
ensembldb from M.musculus NCBI37 v67 gtf
ensembldb
NCBI37
v67
ensembl
6.3 years ago • updated 6.2 years ago
floriandeckert
▴ 30
3
votes
7
replies
3.1k
views
ensDbFromGtf error from gtf file downloaded from GENCODE.
ensembldb
ensdbfromgtf
updated 6.6 years ago by
Johannes Rainer
★ 2.0k • written 6.6 years ago by
Mthabisi Moyo
▴ 40
6
votes
14
replies
2.9k
views
ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTablesFromEnsembl
ensembldb
updated 6.1 years ago by
Johannes Rainer
★ 2.0k • written 6.1 years ago by
Ramiro Magno
▴ 100
0
votes
3
replies
2.9k
views
Can't Install ensembldb and EnsDb.Hsapiens.v86
installation
EnsDb.Hsapiens.v86
Bioconductor
package
ensembldb
22 months ago
elmfinds
• 0
10
votes
18
replies
2.8k
views
ensembldb support for Ensembl's transcript_name column
ensembldb
updated 2.5 years ago by
Hervé Pagès
16k • written 2.5 years ago by
Michael Love
41k
0
votes
5
replies
2.8k
views
mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus.v79
R
annotation
ensembldb
5.5 years ago
foehn
▴ 100
4
votes
4
replies
2.6k
views
Retrieve canonical transcript for each gene via ensembldb R package
annotation
ensembldb
updated 21 months ago by
jon.klonowski
▴ 40 • written 5.3 years ago by
simon.boutry
• 0
2
votes
2
replies
2.6k
views
mapping gene type or biotype to ENSEMBL ID
ensembldb
biomaRt
org.Hs.eg.db
Annotation
updated 3.3 years ago by
Johannes Rainer
★ 2.0k • written 3.3 years ago by
Anubhav
• 0
0
votes
2
replies
2.6k
views
How to get the rsID of 4 million SNPA
ensembldb
SNP
SNPData
genomes
written 2.2 years ago by
Weiqiong
• 0
5
votes
6
replies
2.5k
views
Is mapId supposed to concatenate multiVals?
annotationdbi
ensembldb
updated 6.9 years ago by
Johannes Rainer
★ 2.0k • written 7.0 years ago by
Steve Lianoglou
★ 13k
3
votes
2
replies
2.5k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi
ensembldb
3.2 years ago
Ezgi
▴ 60
2
votes
9
replies
2.4k
views
ensembldb salmon deseq2 txt2import right tool?
ensembldb
deseq2
6.9 years ago
aaron.dickey
• 0
1
vote
2
replies
2.4k
views
Error : object path is not exported by namespace:Rsamtools
packages
installation problem
rsamtools
chippeakanno
ensembldb
6.4 years ago
inzirio
▴ 10
1
vote
2
replies
2.3k
views
tximport using Ensembdb to create Tx2gene dataframe with bovine transcripts ?
tximport
ensembldb
bos taurus
tx2gene
updated 5.8 years ago by
James W. MacDonald
65k • written 5.8 years ago by
gilles.charpigny
• 0
0
votes
3
replies
2.3k
views
incorrect biomaRt output order of gene list
biomart
ensembldb
error
6.2 years ago
Yuqia
• 0
6
votes
10
replies
2.3k
views
ensembldb: ensDbFromGtf error with ensembl version 74
ensembldb
updated 8.0 years ago by
Johannes Rainer
★ 2.0k • written 8.0 years ago by
stianlagstad
▴ 90
2
votes
3
replies
2.2k
views
GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi
GO
clusterProfiler
enrichplot
ensembldb
updated 19 months ago by
merv
▴ 120 • written 19 months ago by
simone.nevills
▴ 10
4
votes
9
replies
2.1k
views
keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
ensdb.hsapiens.v75
ensembldb
keys
updated 7.0 years ago by
Johannes Rainer
★ 2.0k • written 7.0 years ago by
enricoferrero
▴ 660
0
votes
5
replies
2.0k
views
Error when annotating ENSEMBLE transcript IDs from chicken annotation DB
R
ensembldb
Annotation
updated 18 months ago by
Guido Hooiveld
★ 3.9k • written 18 months ago by
Mohamed
▴ 30
0
votes
5
replies
2.0k
views
error when using ensembldb with a MySQL server
ensembldb
rmysql
updated 6.3 years ago by
James W. MacDonald
65k • written 6.3 years ago by
Didi
▴ 10
1
vote
9
replies
1.9k
views
How to filter EnsDb into another EnsDb object instead of GRange?
ens
ensembldb
EnsDb.Hsapiens.v86
EnsDb.Rnorvegicus.v75
2.9 years ago
Ahdee
▴ 50
0
votes
3
replies
1.8k
views
errors with makeTxDbFromBiomart
biomart
genomicfeatures
maketxdbfrombiomart
ensembldb
ensDbFromGtf
updated 6.8 years ago by
Johannes Rainer
★ 2.0k • written 6.8 years ago by
Marie
• 0
5
votes
3
replies
1.7k
views
Is it possible to get Ensembl gene descriptions with ensembldb?
ensembldb
updated 6.9 years ago by
Johannes Rainer
★ 2.0k • written 6.9 years ago by
Julien Roux
▴ 90
0
votes
2
replies
1.7k
views
Generating database with non model species to be use by ReportingTools
reportingtools
annotationdbi
annotationhub
ensembldb
updated 7.9 years ago by
Johannes Rainer
★ 2.0k • written 7.9 years ago by
cagenet34
▴ 20
2
votes
3
replies
1.7k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal
ensembldb
rtracklayer
Annotation
updated 15 months ago by
rbj
• 0 • written 17 months ago by
Jake
▴ 10
2
votes
3
replies
1.7k
views
biomart query in R is not matching ensembl website - missing results
ensembldb
biomaRt
updated 2.6 years ago by
Mike Smith
★ 6.5k • written 2.6 years ago by
Alice
• 0
0
votes
1
reply
1.7k
views
ensembldb package installation issue
ensembldb
package
installation
BiocManager
updated 3.8 years ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
dylangagler
• 0
2
votes
12
replies
1.7k
views
BioFileCache Problem and not linking to ensembldb problem in TxiMeta
Tximeta
BioFileCache
Ensembldb
updated 4.2 years ago by
Martin Morgan
25k • written 4.2 years ago by
kavator
▴ 30
4
votes
2
replies
1.6k
views
News:
ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb
ensembldb
annotation
AnnotationHub
News
3.7 years ago
Johannes Rainer
★ 2.0k
0
votes
1
reply
1.6k
views
ChIPSeeker with Ensembl IDs
chipseeker
Ensembl
EnsDb.Mmusculus.v79
ensembldb
4.1 years ago
Assa Yeroslaviz
★ 1.5k
3
votes
2
replies
1.6k
views
tximport with versioned identifiers
tximport
ensembldb
6.5 years ago
Ed Siefker
▴ 230
0
votes
1
reply
1.5k
views
News:
News:Ensembl 110 has been released
ensembldb
biomaRt
updated 9 months ago by
Michael Love
41k • written 9 months ago by
Benjamin
▴ 30
1
vote
3
replies
1.4k
views
how to get intron with ensembldb. package?
granges
ensembldb
GenomicFeatures
6.3 years ago
alessandro.pastore
▴ 20
5
votes
3
replies
1.4k
views
Problem obtaining NCBI gene IDs from Ensembl version 107
biomaRt
ensembldb
ensembl
18 months ago • updated 15 months ago
jamie.gearing
▴ 60
2
votes
1
reply
1.4k
views
Retrieve gene description with ensembldb
biomaRt
ensembldb
AnnotationData
updated 3.1 years ago by
Johannes Rainer
★ 2.0k • written 3.1 years ago by
António Miguel de Jesus Domingues
▴ 510
0
votes
2
replies
1.4k
views
Can't convert dog ensembl IDs into gene names
biomaRt
ensembldb
updated 2.4 years ago by
ATpoint
★ 4.1k • written 2.4 years ago by
4214811
• 0
1
vote
0
replies
1.4k
views
News:
Ensembl 91 EnsDb databases added to AnnotationHub
annotation
ensembldb
ensembl
News
6.4 years ago
Johannes Rainer
★ 2.0k
3
votes
1
reply
1.3k
views
Mouse to Human Genes using bioconductor
ensembldb
updated 9 months ago by
James W. MacDonald
65k • written 9 months ago by
Max
▴ 10
0
votes
3
replies
1.3k
views
Error: package or namespace load failed for 'EnsDb.Mmusculus.v79'
EnsDb.Mmusculus.v79
EnsDb.Mmusculus.v75
ensembldb
updated 2.4 years ago by
Johannes Rainer
★ 2.0k • written 2.4 years ago by
kelvin
• 0
0
votes
2
replies
1.3k
views
News:
Ensembl 103 has been released
biomaRt
ensembldb
Ensembl
ensemblVEP
Biomart
3.2 years ago • updated 3.0 years ago
mchakiachvili
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2 and Normalization of RNA sequencing data
by
kcarey
• 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP
by
Gordon Smyth
50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma
by
Gordon Smyth
50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
Gordon Smyth
50k
You have discovered something that I have pointed out many times on this forum. fgsea does not implement the classic GSEA method published …
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
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Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
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Answer: DEseq2 coefficient
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