Showing : ensembldb • reset
0
votes
3
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141
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Error using old ensembldb annotations with R 4.0 +
anno EnsDb.Hsapiens.v79 ensDb.HSapiens.v92 AnnotationDbi ensembldb
5 weeks ago rbenel ▴ 20
1
vote
9
replies
290
views
How to filter EnsDb into another EnsDb object instead of GRange?
ens ensembldb EnsDb.Hsapiens.v86 EnsDb.Rnorvegicus.v75
3 months ago Ahdee ▴ 50
1
vote
0
replies
167
views
News: Ensembl 104 has just been released!
ensembldb biomaRt
4 months ago mchakiachvili ▴ 10
2
votes
1
reply
168
views
Retrieve gene description with ensembldb
biomaRt ensembldb AnnotationData
updated 5 months ago by ★ 1.9k • written 5 months ago by ▴ 480
1
vote
2
replies
195
views
Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb RNASeq
5 months ago Torkel • 0
0
votes
2
replies
294
views
News: Ensembl 103 has been released
biomaRt ensembldb Ensembl ensemblVEP Biomart
7 months ago • updated 4 months ago mchakiachvili ▴ 10
3
votes
2
replies
290
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
7 months ago Ezgi ▴ 30
0
votes
2
replies
315
views
mapping gene type or biotype to ENSEMBL ID
ensembldb biomaRt org.Hs.eg.db Annotation
updated 8 months ago by ★ 1.9k • written 8 months ago by • 0
1
vote
1
reply
198
views
topGO question
Ensembl ensembldb
updated 9 months ago by 58k • written 9 months ago by • 0
0
votes
0
replies
201
views
News: Ensembl 102 has been released
Ensembl biomaRt BioMar ensembldb
9 months ago mchakiachvili ▴ 10
0
votes
4
replies
265
views
Gene information (GRanges + sequence) to GenBank
granges genomic ranges genbankr ensembldb
updated 11 months ago by 58k • written 11 months ago by ▴ 20
4
votes
2
replies
322
views
News: ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb ensembldb annotation AnnotationHub News
12 months ago Johannes Rainer ★ 1.9k
0
votes
1
reply
318
views
ensembldb package installation issue
ensembldb package installation BiocManager
updated 13 months ago by 3.4k • written 13 months ago by • 0
1
vote
1
reply
186
views
Is transcript color accessible through ensembldb? (gold = in both HAVANA+ENSEMBL)
ensembldb
updated 14 months ago by ★ 1.9k • written 14 months ago by ▴ 120
1
vote
0
replies
264
views
News: ensembldb EnsDb databases for Ensembl release 100 added to AnnotationHub
ensembl annotation ensembldb News
16 months ago Johannes Rainer ★ 1.9k
2
votes
1
reply
180
views
protein_domain_source from ensembldb and mapping with PFAM.db
ensembldb pfam.db
17 months ago bruce.moran ▴ 30
0
votes
1
reply
324
views
ChIPSeeker with Ensembl IDs
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb
17 months ago Assa Yeroslaviz ★ 1.5k
2
votes
12
replies
361
views
BioFileCache Problem and not linking to ensembldb problem in TxiMeta
Tximeta BioFileCache Ensembldb
updated 19 months ago by 25k • written 19 months ago by ▴ 20
3
votes
0
replies
273
views
News: EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation ensembldb EnsDb AnnotationHub News
22 months ago Johannes Rainer ★ 1.9k
5
votes
6
replies
1.0k
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 23 months ago by ★ 2.7k • written 23 months ago by ▴ 80
1
vote
0
replies
311
views
News: ensembldb EnsDb databases for Ensembl release 97 added to AnnotationHub
annotation ensembldb Ensembl News
2.2 years ago Johannes Rainer ★ 1.9k
1
vote
1
reply
640
views
Retrieve canonical transcript for each gene via ensembldb R package
annotation ensembldb
updated 2.6 years ago by ★ 1.9k • written 2.7 years ago by • 0
7
votes
8
replies
1.5k
views
R failing to load genome files from EnsDb.Hsapiens.v86
tximport ensembldb EnsDB.hsapiens.v86
updated 2.7 years ago by 0 • written 2.8 years ago by ▴ 20
0
votes
1
reply
407
views
Pick coding vs non-coding from Ensembl data set
R ensembl ensembldb noncoding rna protein coding
updated 2.8 years ago by ★ 1.9k • written 2.8 years ago by • 0
5
votes
10
replies
988
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 8 months ago by ★ 1.9k • written 2.8 years ago by ★ 3.0k
0
votes
5
replies
983
views
mitochodria isCircular equals to FALSE in EnsDb.Hsapiens.v86 and EnsDb.Mmusculus.v79
R annotation ensembldb
2.9 years ago foehn ▴ 80
1
vote
2
replies
1.1k
views
tximport using Ensembdb to create Tx2gene dataframe with bovine transcripts ?
tximport ensembldb bos taurus tx2gene
updated 3.1 years ago by 58k • written 3.1 years ago by • 0
0
votes
3
replies
1.2k
views
Create Ensembl transcript to gene IDs table with R ensembldb package for tximport
ensembldb tximport salmon
updated 3.3 years ago by ★ 1.9k • written 3.3 years ago by ▴ 30
6
votes
14
replies
1.1k
views
ensembldb error/bug: Can't locate Bio/EnsEMBL/ApiVersion.pm in @INC | fetchTablesFromEnsembl
ensembldb
updated 3.4 years ago by ★ 1.9k • written 3.4 years ago by ▴ 100
0
votes
3
replies
1.2k
views
incorrect biomaRt output order of gene list
biomart ensembldb error
3.5 years ago Yuqia • 0
2
votes
4
replies
5.1k
views
converting ensembl transcript ID to ensemble gene: problem & missing values
biomart error ensembldb
3.6 years ago • updated 3.5 years ago Yuqia • 0
6
votes
11
replies
1.5k
views
ensembldb from M.musculus NCBI37 v67 gtf
ensembldb NCBI37 v67 ensembl
3.6 years ago floriandeckert ▴ 30
5
votes
9
replies
1.8k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
3.6 years ago emmak ▴ 20
1
vote
3
replies
815
views
how to get intron with ensembldb. package?
granges ensembldb GenomicFeatures
3.7 years ago alessandro.pastore ▴ 20
2
votes
2
replies
542
views
ensembldb and pseudogenes mapping to the same Ensembl ID
ensembldb
3.7 years ago meeta.mistry ▴ 20
0
votes
5
replies
894
views
error when using ensembldb with a MySQL server
ensembldb rmysql
updated 3.7 years ago by 58k • written 3.7 years ago by ▴ 10
1
vote
0
replies
919
views
News: Ensembl 91 EnsDb databases added to AnnotationHub
annotation ensembldb ensembl News
3.7 years ago Johannes Rainer ★ 1.9k
1
vote
2
replies
1.3k
views
Error : object path is not exported by namespace:Rsamtools
packages installation problem rsamtools chippeakanno ensembldb
3.7 years ago inzirio ▴ 10
1
vote
2
replies
684
views
get_gene_transcript_exon_tables.pl extremely slow
ensembl ensembldb
updated 3.9 years ago by ★ 1.9k • written 3.9 years ago by ▴ 230
3
votes
2
replies
713
views
tximport with versioned identifiers
tximport ensembldb
3.9 years ago Ed Siefker ▴ 230
3
votes
7
replies
1.4k
views
ensDbFromGtf error from gtf file downloaded from GENCODE.
ensembldb ensdbfromgtf
updated 4.0 years ago by ★ 1.9k • written 4.0 years ago by ▴ 30
3
votes
8
replies
2.2k
views
EnsemblDb: how to retrieve gene name / description?
EnsDb.Mmusculus.v79 ensembldb annotation
updated 4.1 years ago by ★ 1.9k • written 4.1 years ago by ★ 3.0k
0
votes
3
replies
1.1k
views
errors with makeTxDbFromBiomart
biomart genomicfeatures maketxdbfrombiomart ensembldb ensDbFromGtf
updated 4.1 years ago by ★ 1.9k • written 4.1 years ago by • 0
5
votes
3
replies
875
views
Is it possible to get Ensembl gene descriptions with ensembldb?
ensembldb
updated 4.3 years ago by ★ 1.9k • written 4.3 years ago by ▴ 90
2
votes
9
replies
1.3k
views
ensembldb salmon deseq2 txt2import right tool?
ensembldb deseq2
4.3 years ago aaron.dickey • 0
5
votes
6
replies
889
views
Is mapId supposed to concatenate multiVals?
annotationdbi ensembldb
updated 4.3 years ago by ★ 1.9k • written 4.3 years ago by 13k
4
votes
9
replies
1.1k
views
keys() fails on EnsDb.Hsapiens.v75 on Bioc 3.5
ensdb.hsapiens.v75 ensembldb keys
updated 4.3 years ago by ★ 1.9k • written 4.3 years ago by ▴ 570
0
votes
2
replies
819
views
Generating database with non model species to be use by ReportingTools
reportingtools annotationdbi annotationhub ensembldb
updated 5.2 years ago by ★ 1.9k • written 5.2 years ago by ▴ 20
0
votes
2
replies
672
views
ENSEMBL_MART_FUNCGEN not accessible through biomaRt?
biomart regulatory ensemble mart ensembldb
updated 5.3 years ago by ▴ 790 • written 5.3 years ago by ▴ 50
6
votes
10
replies
1.2k
views
ensembldb: ensDbFromGtf error with ensembl version 74
ensembldb
updated 5.3 years ago by ★ 1.9k • written 5.3 years ago by ▴ 90
50 results • Page 1 of 1
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Replies
Answer: Error in makeTxDbFromGFF(txomeInfo$gtf) by Michael Love 34k
I see that tximeta found a linked transcriptome. Can you show this part of your code as well? How did you create the `linkedTxome`?
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Gordon Smyth 43k
You need to start by doing an ordinary paired analysis.
Comment: Recalculated abundance data output table with DEseq2 by Michael Love 34k
Yes, DESeq() then results(). When you print the table it will say MLE. No we don’t have a function to do that.
Comment: Recalculated abundance data output table with DEseq2 by michael.morash • 0
Thanks for getting back to me so quickly. The final comparison we are looking to report are the effects of filtering out low count genes us…
Comment: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi by Field -Ye • 0
Hi Professor Smyth, Thank you for pointing me to your previous publication. I went through the verbal part and found you did pursue the DG…
Votes
Answer: Degust: what normalization method does it use
Answer: ylim and xlim in Enhanced Volcano
Answer: EdgeR, tumor normal pair, no replicatie but multiple patients, to focus on indi
Error in .rowNamesDF<-(x, value = value) :duplicate row.names are not allowed DESeq2
Comment: How to build a GRangesList where each GRanges element is a CDS coordinate of gen
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