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ensembldb
•
reset
2
votes
0
replies
74
views
News:
News:Ensembl 106 has just been released!
ensembl
biomaRt
ensembldb
4 weeks ago
Benjamin
▴ 20
2
votes
2
replies
140
views
ensembldb to make the EnsDb for Human Version 105 using 'fetchTablesFromEnsembl' I'm on day two, can it be sped up?
ensembldb
10 weeks ago
Matthew Thornton
▴ 350
0
votes
1
reply
178
views
How to get the rsID of 4 million SNPA
ensembldb
SNP
SNPData
genomes
updated 11 weeks ago by
Kevin Blighe
3.5k • written 11 weeks ago by
Weiqiong
• 0
8
votes
9
replies
703
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 3 months ago by
Hervé Pagès
15k • written 3 months ago by
jon.klonowski
▴ 30
0
votes
2
replies
313
views
Can't convert dog ensembl IDs into gene names
biomaRt
ensembldb
updated 4 months ago by
ATpoint
★ 1.2k • written 4 months ago by
4214811
• 0
0
votes
3
replies
368
views
Error: package or namespace load failed for 'EnsDb.Mmusculus.v79'
EnsDb.Mmusculus.v79
EnsDb.Mmusculus.v75
ensembldb
updated 4 months ago by
Johannes Rainer
★ 1.9k • written 4 months ago by
kelvin
• 0
1
vote
0
replies
146
views
News:
Ensembl 105 has just been released!
ensembl
biomaRt
ensembldb
5 months ago
mchakiachvili
▴ 20
0
votes
0
replies
183
views
How to get Cytogenetic band for muscles gene by using Biomart or other tools in R
Annotation
biomaRt
ensembldb
5 months ago
Liting
• 0
10
votes
18
replies
994
views
ensembldb support for Ensembl's transcript_name column
ensembldb
updated 6 months ago by
Hervé Pagès
15k • written 6 months ago by
Michael Love
36k
0
votes
3
replies
264
views
Problem select / ensembl package
ensembldb
6 months ago
yinnahm
• 0
2
votes
3
replies
398
views
biomart query in R is not matching ensembl website - missing results
ensembldb
biomaRt
updated 7 months ago by
Mike Smith
★ 5.5k • written 7 months ago by
Alice
• 0
0
votes
3
replies
302
views
Error using old ensembldb annotations with R 4.0 +
anno
EnsDb.Hsapiens.v79
ensDb.HSapiens.v92
AnnotationDbi
ensembldb
9 months ago
rbenel
▴ 20
1
vote
9
replies
520
views
How to filter EnsDb into another EnsDb object instead of GRange?
ens
ensembldb
EnsDb.Hsapiens.v86
EnsDb.Rnorvegicus.v75
11 months ago
Ahdee
▴ 50
1
vote
0
replies
345
views
News:
Ensembl 104 has just been released!
ensembldb
biomaRt
12 months ago
mchakiachvili
▴ 20
2
votes
1
reply
314
views
Retrieve gene description with ensembldb
biomaRt
ensembldb
AnnotationData
updated 13 months ago by
Johannes Rainer
★ 1.9k • written 13 months ago by
António Miguel de Jesus Domingues
▴ 480
1
vote
2
replies
342
views
Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb
RNASeq
13 months ago
Torkel
• 0
0
votes
2
replies
520
views
News:
Ensembl 103 has been released
biomaRt
ensembldb
Ensembl
ensemblVEP
Biomart
15 months ago • updated 12 months ago
mchakiachvili
▴ 20
3
votes
2
replies
659
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi
ensembldb
15 months ago
Ezgi
▴ 30
0
votes
2
replies
833
views
mapping gene type or biotype to ENSEMBL ID
ensembldb
biomaRt
org.Hs.eg.db
Annotation
updated 16 months ago by
Johannes Rainer
★ 1.9k • written 16 months ago by
Anubhav
• 0
1
vote
1
reply
375
views
topGO question
Ensembl
ensembldb
updated 17 months ago by
James W. MacDonald
59k • written 17 months ago by
H. Stotz
• 0
0
votes
0
replies
316
views
News:
Ensembl 102 has been released
Ensembl
biomaRt
BioMar
ensembldb
17 months ago
mchakiachvili
▴ 20
0
votes
4
replies
408
views
Gene information (GRanges + sequence) to GenBank
granges
genomic ranges
genbankr
ensembldb
updated 19 months ago by
James W. MacDonald
59k • written 19 months ago by
biomiha
▴ 20
4
votes
2
replies
527
views
News:
ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb
ensembldb
annotation
AnnotationHub
News
20 months ago
Johannes Rainer
★ 1.9k
0
votes
1
reply
595
views
ensembldb package installation issue
ensembldb
package
installation
BiocManager
updated 21 months ago by
Kevin Blighe
3.5k • written 21 months ago by
dylangagler
• 0
1
vote
1
reply
286
views
Is transcript color accessible through ensembldb? (gold = in both HAVANA+ENSEMBL)
ensembldb
updated 22 months ago by
Johannes Rainer
★ 1.9k • written 22 months ago by
Aditya
▴ 140
1
vote
0
replies
395
views
News:
ensembldb EnsDb databases for Ensembl release 100 added to AnnotationHub
ensembl
annotation
ensembldb
News
2.0 years ago
Johannes Rainer
★ 1.9k
2
votes
1
reply
280
views
protein_domain_source from ensembldb and mapping with PFAM.db
ensembldb
pfam.db
2.1 years ago
bruce.moran
▴ 30
0
votes
1
reply
644
views
ChIPSeeker with Ensembl IDs
chipseeker
Ensembl
EnsDb.Mmusculus.v79
ensembldb
2.1 years ago
Assa Yeroslaviz
★ 1.5k
2
votes
12
replies
624
views
BioFileCache Problem and not linking to ensembldb problem in TxiMeta
Tximeta
BioFileCache
Ensembldb
updated 2.2 years ago by
Martin Morgan
25k • written 2.2 years ago by
kavator
▴ 20
3
votes
0
replies
390
views
News:
EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation
ensembldb
EnsDb
AnnotationHub
News
2.5 years ago
Johannes Rainer
★ 1.9k
5
votes
6
replies
1.5k
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 2.6 years ago by
Robert Castelo
★ 2.8k • written 2.6 years ago by
Stephanie Hicks
▴ 80
1
vote
0
replies
406
views
News:
ensembldb EnsDb databases for Ensembl release 97 added to AnnotationHub
annotation
ensembldb
Ensembl
News
2.9 years ago
Johannes Rainer
★ 1.9k
1
vote
1
reply
841
views
Retrieve canonical transcript for each gene via ensembldb R package
annotation
ensembldb
updated 3.3 years ago by
Johannes Rainer
★ 1.9k • written 3.3 years ago by
simon.boutry
• 0
7
votes
8
replies
2.1k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport
ensembldb
EnsDB.hsapiens.v86
updated 3.4 years ago by
Bioconductor Community
0 • written 3.5 years ago by
michaelschoeber
▴ 20
0
votes
1
reply
523
views
Pick coding vs non-coding from Ensembl data set
R
ensembl
ensembldb
noncoding rna
protein coding
updated 3.5 years ago by
Johannes Rainer
★ 1.9k • written 3.5 years ago by
jdmentze
• 0
5
votes
12
replies
1.3k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 2 hours ago by
Johannes Rainer
★ 1.9k • written 3.5 years ago by
Guido Hooiveld
★ 3.2k
0
votes
5
replies
1.5k
views
mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus.v79
R
annotation
ensembldb
3.5 years ago
foehn
▴ 80
1
vote
2
replies
1.4k
views
tximport using Ensembdb to create Tx2gene dataframe with bovine transcripts ?
tximport
ensembldb
bos taurus
tx2gene
updated 3.8 years ago by
James W. MacDonald
59k • written 3.8 years ago by
gilles.charpigny
• 0
0
votes
3
replies
2.0k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb
tximport
salmon
updated 4.0 years ago by
Johannes Rainer
★ 1.9k • written 4.0 years ago by
user31888
▴ 30
6
votes
14
replies
1.5k
views
ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTablesFromEnsembl
ensembldb
updated 4.1 years ago by
Johannes Rainer
★ 1.9k • written 4.1 years ago by
Ramiro Magno
▴ 100
0
votes
3
replies
1.4k
views
incorrect biomaRt output order of gene list
biomart
ensembldb
error
4.2 years ago
Yuqia
• 0
2
votes
4
replies
6.4k
views
converting ensembl transcript ID to ensemble gene: problem & missing values
biomart
error
ensembldb
4.2 years ago
Yuqia
• 0
6
votes
11
replies
1.7k
views
ensembldb from M.musculus NCBI37 v67 gtf
ensembldb
NCBI37
v67
ensembl
4.3 years ago
floriandeckert
▴ 30
5
votes
9
replies
2.1k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb
ensembl release
rnaseq
salmon
tximport
4.3 years ago
emmak
▴ 20
1
vote
3
replies
947
views
how to get intron with ensembldb. package?
granges
ensembldb
GenomicFeatures
4.3 years ago
alessandro.pastore
▴ 20
2
votes
2
replies
693
views
ensembldb and pseudogenes mapping to the same Ensembl ID
ensembldb
4.4 years ago
meeta.mistry
▴ 20
0
votes
5
replies
1.3k
views
error when using ensembldb with a MySQL server
ensembldb
rmysql
updated 4.4 years ago by
James W. MacDonald
59k • written 4.4 years ago by
Didi
▴ 10
1
vote
0
replies
1.0k
views
News:
Ensembl 91 EnsDb databases added to AnnotationHub
annotation
ensembldb
ensembl
News
4.4 years ago
Johannes Rainer
★ 1.9k
1
vote
2
replies
1.5k
views
Error : object path is not exported by namespace:Rsamtools
packages
installation problem
rsamtools
chippeakanno
ensembldb
4.4 years ago
inzirio
▴ 10
1
vote
2
replies
780
views
get_gene_transcript_exon_tables.pl extremely slow
ensembl
ensembldb
updated 4.5 years ago by
Johannes Rainer
★ 1.9k • written 4.5 years ago by
Ed Siefker
▴ 230
50 results • Page
1 of 1
Recent ...
Replies
Comment: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
by
Yang Shi
• 0
Perfect answer! This questions troubled me for a long time. Thanks again and for your quick and detailed reply.
Comment: HTSeq Counts no longer available
by
swbarnes2
★ 1.0k
STAR's output was intended to mimic HTseq-counts.
Answer: Methods for removing unexpressed probes of Human Transcriptome Array HTA 2.0
by
James W. MacDonald
59k
In the previous post I noted that `paCalls` doesn't exist for this array, and that is still true today. And there are no methods similar to…
Comment: DiffBind GreyListChIP error: Error: BiocParallel errors
by
Rory Stark
★ 4.4k
Could you let me know the versions? Output of `sessionInfo()`.
Comment: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o
by
Yang Shi
• 0
okay sir, the new post is here (https://support.bioconductor.org/p/9144266/). Looking forward to your reply.
Votes
Answer: Variance explained (coefficient of determination) in edgeR
HTSeq Counts no longer available
Comment: Problem converting transcript to genomic coordinates with Annotation Hub
Comment: Separate exogenous from endogenous transcripts using Salmon RNAseq DTU
C: Appropriate pre-processing pipeline for Human Transcriptome Array HTA 2.0 with o
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