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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
6.0k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 9 weeks ago by
shepherl
3.9k • written 2.3 years ago by
jon.klonowski
▴ 40
7
votes
39
replies
5.8k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 18 hours ago by
Daniele
• 0 • written 5.5 years ago by
Guido Hooiveld
★ 4.0k
3
votes
8
replies
4.4k
views
EnsemblDb: how to retrieve gene name / description?
EnsDb.Mmusculus.v79
ensembldb
annotation
updated 6.8 years ago by
Johannes Rainer
★ 2.0k • written 6.8 years ago by
Guido Hooiveld
★ 4.0k
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
4.3k
views
Conversion of UniProt to Ensembl
biomaRt
ensembldb
UniProt.ws
updated 7 months ago by
Marcel Ramos
700 • written 21 months ago by
Recep
▴ 20
7
votes
8
replies
3.8k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport
ensembldb
EnsDB.hsapiens.v86
updated 5.4 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
6.3 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
floriandeckert
▴ 30
3
votes
7
replies
3.1k
views
ensDbFromGtf error from gtf file downloaded from GENCODE.
ensembldb
ensdbfromgtf
updated 6.7 years ago by
Johannes Rainer
★ 2.0k • written 6.7 years ago by
Mthabisi Moyo
▴ 40
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
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
10
votes
18
replies
2.9k
views
ensembldb support for Ensembl's transcript_name column
ensembldb
updated 2.5 years ago by
Hervé Pagès
16k • written 2.6 years ago by
Michael Love
42k
0
votes
5
replies
2.8k
views
mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus.v79
R
annotation
ensembldb
5.6 years ago
foehn
▴ 100
4
votes
4
replies
2.7k
views
Retrieve canonical transcript for each gene via ensembldb R package
annotation
ensembldb
updated 22 months ago by
jon.klonowski
▴ 40 • written 5.3 years ago by
simon.boutry
• 0
0
votes
2
replies
2.7k
views
How to get the rsID of 4 million SNPA
ensembldb
SNP
SNPData
genomes
written 2.2 years ago by
Weiqiong
• 0
2
votes
2
replies
2.6k
views
mapping gene type or biotype to ENSEMBL ID
ensembldb
biomaRt
org.Hs.eg.db
Annotation
updated 3.4 years ago by
Johannes Rainer
★ 2.0k • written 3.4 years ago by
Anubhav
• 0
3
votes
2
replies
2.5k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi
ensembldb
3.3 years ago
Ezgi
▴ 60
5
votes
6
replies
2.5k
views
Is mapId supposed to concatenate multiVals?
annotationdbi
ensembldb
updated 7.0 years ago by
Johannes Rainer
★ 2.0k • written 7.0 years ago by
Steve Lianoglou
★ 13k
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
2
votes
3
replies
2.3k
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 20 months ago by
simone.nevills
▴ 10
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
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
2.1k
views
Error when annotating ENSEMBLE transcript IDs from chicken annotation DB
R
ensembldb
Annotation
updated 19 months ago by
Guido Hooiveld
★ 4.0k • written 19 months ago by
Mohamed
▴ 30
0
votes
5
replies
2.0k
views
error when using ensembldb with a MySQL server
ensembldb
rmysql
updated 6.4 years ago by
James W. MacDonald
65k • written 6.4 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
3.0 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
0
votes
2
replies
1.8k
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
5
votes
3
replies
1.8k
views
Is it possible to get Ensembl gene descriptions with ensembldb?
ensembldb
updated 6.9 years ago by
Johannes Rainer
★ 2.0k • written 7.0 years ago by
Julien Roux
▴ 90
2
votes
3
replies
1.8k
views
Packages dependent on rtracklayer fail: ERROR: lazy loading failed, unable to load shared object rtracklayer.so
SingleCellMultiModal
ensembldb
rtracklayer
Annotation
updated 16 months ago by
rbj
• 0 • written 18 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
1.7k
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
6.6 years ago
Ed Siefker
▴ 230
0
votes
1
reply
1.6k
views
News:
News:Ensembl 110 has been released
ensembldb
biomaRt
updated 10 months ago by
Michael Love
42k • written 10 months ago by
Benjamin
▴ 30
5
votes
3
replies
1.5k
views
Problem obtaining NCBI gene IDs from Ensembl version 107
biomaRt
ensembldb
ensembl
19 months ago • updated 16 months ago
jamie.gearing
▴ 60
2
votes
1
reply
1.5k
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
1
vote
3
replies
1.4k
views
how to get intron with ensembldb. package?
granges
ensembldb
GenomicFeatures
6.3 years ago
alessandro.pastore
▴ 20
3
votes
1
reply
1.4k
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
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
0
votes
3
replies
1.4k
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
3.3 years ago • updated 3.1 years ago
mchakiachvili
▴ 20
50 results • Page
1 of 1
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons
by
Michael Love
42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs
by
Michael Love
42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons
by
swbarnes2
★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs
by
shaunpeterson
• 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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