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ensembldb
•
reset
0
votes
3
replies
1.6k
views
Error using old ensembldb annotations with R 4.0 +
anno
EnsDb.Hsapiens.v79
ensDb.HSapiens.v92
AnnotationDbi
ensembldb
4.1 years ago
rbenel
▴ 50
1
vote
9
replies
2.9k
views
How to filter EnsDb into another EnsDb object instead of GRange?
ens
ensembldb
EnsDb.Hsapiens.v86
EnsDb.Rnorvegicus.v75
4.3 years ago
Ahdee
▴ 60
1
vote
0
replies
1.4k
views
News:
Ensembl 104 has just been released!
ensembldb
biomaRt
4.3 years ago
mchakiachvili
▴ 20
2
votes
1
reply
2.8k
views
Retrieve gene description with ensembldb
biomaRt
ensembldb
AnnotationData
updated 4.4 years ago by
Johannes Rainer
★ 2.1k • written 4.4 years ago by
António Miguel de Jesus Domingues
▴ 510
1
vote
2
replies
1.6k
views
Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb
RNASeq
4.4 years ago
Torkel
• 0
0
votes
2
replies
1.9k
views
News:
Ensembl 103 has been released
biomaRt
ensembldb
Ensembl
ensemblVEP
Biomart
4.6 years ago • updated 4.4 years ago
mchakiachvili
▴ 20
3
votes
2
replies
4.1k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi
ensembldb
4.6 years ago
Ezgi
▴ 60
2
votes
2
replies
4.7k
views
mapping gene type or biotype to ENSEMBL ID
ensembldb
biomaRt
org.Hs.eg.db
Annotation
updated 4.7 years ago by
Johannes Rainer
★ 2.1k • written 4.7 years ago by
Anubhav
• 0
1
vote
1
reply
1.8k
views
topGO question
Ensembl
ensembldb
updated 4.8 years ago by
James W. MacDonald
68k • written 4.8 years ago by
H. Stotz
• 0
0
votes
0
replies
1.1k
views
News:
Ensembl 102 has been released
Ensembl
biomaRt
BioMar
ensembldb
4.8 years ago
mchakiachvili
▴ 20
0
votes
4
replies
1.9k
views
Gene information (GRanges + sequence) to GenBank
granges
genomic ranges
genbankr
ensembldb
updated 4.9 years ago by
James W. MacDonald
68k • written 4.9 years ago by
biomiha
▴ 20
4
votes
2
replies
2.3k
views
News:
ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb
ensembldb
annotation
AnnotationHub
News
5.0 years ago
Johannes Rainer
★ 2.1k
0
votes
1
reply
2.5k
views
ensembldb package installation issue
ensembldb
package
installation
BiocManager
updated 5.1 years ago by
Kevin Blighe
★ 4.0k • written 5.1 years ago by
dylangagler
• 0
1
vote
1
reply
1.0k
views
Is transcript color accessible through ensembldb? (gold = in both HAVANA+ENSEMBL)
ensembldb
updated 5.2 years ago by
Johannes Rainer
★ 2.1k • written 5.2 years ago by
Aditya
▴ 160
1
vote
0
replies
1.6k
views
News:
ensembldb EnsDb databases for Ensembl release 100 added to AnnotationHub
ensembl
annotation
ensembldb
News
5.3 years ago
Johannes Rainer
★ 2.1k
2
votes
1
reply
1.3k
views
protein_domain_source from ensembldb and mapping with PFAM.db
ensembldb
pfam.db
5.4 years ago
bruce.moran
▴ 30
0
votes
1
reply
2.1k
views
ChIPSeeker with Ensembl IDs
chipseeker
Ensembl
EnsDb.Mmusculus.v79
ensembldb
5.4 years ago
Assa Yeroslaviz
★ 1.5k
2
votes
12
replies
2.3k
views
BioFileCache Problem and not linking to ensembldb problem in TxiMeta
Tximeta
BioFileCache
Ensembldb
updated 5.6 years ago by
Martin Morgan
25k • written 5.6 years ago by
kavator
▴ 30
3
votes
0
replies
1.7k
views
News:
EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation
ensembldb
EnsDb
AnnotationHub
News
5.8 years ago
Johannes Rainer
★ 2.1k
5
votes
6
replies
4.8k
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 5.9 years ago by
Robert Castelo
★ 3.4k • written 5.9 years ago by
Stephanie Hicks
▴ 80
1
vote
0
replies
1.2k
views
News:
ensembldb EnsDb databases for Ensembl release 97 added to AnnotationHub
annotation
ensembldb
Ensembl
News
6.2 years ago
Johannes Rainer
★ 2.1k
4
votes
4
replies
3.9k
views
Retrieve canonical transcript for each gene via ensembldb R package
annotation
ensembldb
updated 3.1 years ago by
jon.klonowski
▴ 40 • written 6.6 years ago by
simon.boutry
• 0
7
votes
8
replies
5.0k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport
ensembldb
EnsDB.hsapiens.v86
updated 6.7 years ago by
Bioconductor Community
0 • written 6.8 years ago by
michaelschoeber
▴ 20
0
votes
1
reply
1.4k
views
Pick coding vs non-coding from Ensembl data set
R
ensembl
ensembldb
noncoding rna
protein coding
updated 6.8 years ago by
Johannes Rainer
★ 2.1k • written 6.8 years ago by
jdmentze
• 0
0
votes
5
replies
3.5k
views
mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus.v79
R
annotation
ensembldb
6.9 years ago
foehn
▴ 100
1
vote
2
replies
2.8k
views
tximport using Ensembdb to create Tx2gene dataframe with bovine transcripts ?
tximport
ensembldb
bos taurus
tx2gene
updated 7.1 years ago by
James W. MacDonald
68k • written 7.1 years ago by
gilles.charpigny
• 0
0
votes
3
replies
5.2k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb
tximport
salmon
updated 7.3 years ago by
Johannes Rainer
★ 2.1k • written 7.3 years ago by
user31888
▴ 30
6
votes
14
replies
3.8k
views
ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTablesFromEnsembl
ensembldb
updated 7.4 years ago by
Johannes Rainer
★ 2.1k • written 7.4 years ago by
Ramiro Magno
▴ 100
0
votes
3
replies
2.9k
views
incorrect biomaRt output order of gene list
biomart
ensembldb
error
7.5 years ago
Yuqia
• 0
3
votes
4
replies
17k
views
converting ensembl transcript ID to ensemble gene: problem & missing values
biomart
error
ensembldb
7.5 years ago
Yuqia
• 0
6
votes
11
replies
4.2k
views
ensembldb from M.musculus NCBI37 v67 gtf
ensembldb
NCBI37
v67
ensembl
7.6 years ago
floriandeckert
▴ 30
5
votes
9
replies
4.2k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb
ensembl release
rnaseq
salmon
tximport
7.6 years ago
emmak
▴ 20
1
vote
3
replies
1.8k
views
how to get intron with ensembldb. package?
granges
ensembldb
GenomicFeatures
7.6 years ago
alessandro.pastore
▴ 20
2
votes
2
replies
1.8k
views
ensembldb and pseudogenes mapping to the same Ensembl ID
ensembldb
7.7 years ago
meeta.mistry
▴ 30
0
votes
5
replies
2.4k
views
error when using ensembldb with a MySQL server
ensembldb
rmysql
updated 7.7 years ago by
James W. MacDonald
68k • written 7.7 years ago by
Didi
▴ 10
1
vote
0
replies
1.6k
views
News:
Ensembl 91 EnsDb databases added to AnnotationHub
annotation
ensembldb
ensembl
News
7.7 years ago
Johannes Rainer
★ 2.1k
1
vote
2
replies
3.0k
views
Error : object path is not exported by namespace:Rsamtools
packages
installation problem
rsamtools
chippeakanno
ensembldb
7.7 years ago
inzirio
▴ 10
1
vote
2
replies
1.6k
views
get_gene_transcript_exon_tables.pl extremely slow
ensembl
ensembldb
updated 7.9 years ago by
Johannes Rainer
★ 2.1k • written 7.9 years ago by
Ed Siefker
▴ 230
3
votes
2
replies
1.9k
views
tximport with versioned identifiers
tximport
ensembldb
7.9 years ago
Ed Siefker
▴ 230
3
votes
7
replies
4.0k
views
ensDbFromGtf error from gtf file downloaded from GENCODE.
ensembldb
ensdbfromgtf
updated 8.0 years ago by
Johannes Rainer
★ 2.1k • written 8.0 years ago by
Mthabisi Moyo
▴ 40
3
votes
8
replies
6.0k
views
EnsemblDb: how to retrieve gene name / description?
EnsDb.Mmusculus.v79
ensembldb
annotation
updated 8.1 years ago by
Johannes Rainer
★ 2.1k • written 8.1 years ago by
Guido Hooiveld
★ 4.1k
0
votes
3
replies
2.1k
views
errors with makeTxDbFromBiomart
biomart
genomicfeatures
maketxdbfrombiomart
ensembldb
ensDbFromGtf
updated 8.1 years ago by
Johannes Rainer
★ 2.1k • written 8.1 years ago by
Marie
• 0
5
votes
3
replies
2.2k
views
Is it possible to get Ensembl gene descriptions with ensembldb?
ensembldb
updated 8.2 years ago by
Johannes Rainer
★ 2.1k • written 8.3 years ago by
Julien Roux
▴ 90
2
votes
9
replies
3.0k
views
ensembldb salmon deseq2 txt2import right tool?
ensembldb
deseq2
8.3 years ago
aaron.dickey
• 0
5
votes
6
replies
3.8k
views
Is mapId supposed to concatenate multiVals?
annotationdbi
ensembldb
updated 8.3 years ago by
Johannes Rainer
★ 2.1k • written 8.3 years ago by
Steve Lianoglou
★ 13k
4
votes
9
replies
2.7k
views
keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
ensdb.hsapiens.v75
ensembldb
keys
updated 8.3 years ago by
Johannes Rainer
★ 2.1k • written 8.3 years ago by
enricoferrero
▴ 680
0
votes
2
replies
2.4k
views
Generating database with non model species to be use by ReportingTools
reportingtools
annotationdbi
annotationhub
ensembldb
updated 9.2 years ago by
Johannes Rainer
★ 2.1k • written 9.2 years ago by
cagenet34
▴ 20
0
votes
2
replies
1.4k
views
ENSEMBL_MART_FUNCGEN not accessible through biomaRt?
biomart
regulatory
ensemble mart
ensembldb
updated 9.2 years ago by
Thomas Maurel
▴ 800 • written 9.2 years ago by
Sigve Nakken
▴ 50
6
votes
10
replies
3.2k
views
ensembldb: ensDbFromGtf error with ensembl version 74
ensembldb
updated 9.3 years ago by
Johannes Rainer
★ 2.1k • written 9.3 years ago by
stianlagstad
▴ 90
5
votes
1
reply
3.8k
views
Tutorial:
Prototyping An Analysis Pipeline For Lexogen 3'-UTR RNA-seq In Bioconductor
shortread
rsubread
ensembldb
Tutorial
9.4 years ago
phil.chapman
▴ 150
100 results • Page
2 of 2
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Replies
Comment: org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key
by
thundernight
• 0
I'm actually having the same problem. [Spanish dictionary][1] [1]: https://spanishdictionary.cc
Comment: voomLmFit fitted log-CPM values
by
Gordon Smyth
53k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
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Lina
▴ 10
Is the output from fitted(v) in the log2 CPM scale? or CPM scale?
Answer: voomLmFit fitted log-CPM values
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Gordon Smyth
53k
Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```
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• 0
What specific requirements should be noted when preparing abstracts for presentation formats such as short talks, package demos, or posters…
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How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
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