Showing : ensembldb • reset
6
votes
11
replies
3.2k
views
ensembldb from M.musculus NCBI37 v67 gtf
ensembldb NCBI37 v67 ensembl
6.3 years ago floriandeckert ▴ 30
7
votes
39
replies
5.8k
views
Ensembl plants at annotationHub?
ensembl ensembldb plant arabidopsis thaliana annotationhub
updated 18 hours ago by • 0 • written 5.5 years ago by ★ 4.0k
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 ★ 3.3k • written 4.6 years ago by ▴ 80
5
votes
3
replies
1.8k
views
Is it possible to get Ensembl gene descriptions with ensembldb?
ensembldb
updated 6.9 years ago by ★ 2.0k • written 7.0 years ago by ▴ 90
9
votes
11
replies
6.0k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl Rstudio ensembldb AnnotationHub ensdb
updated 9 weeks ago by 3.9k • written 2.3 years ago by ▴ 40
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
0
votes
3
replies
2.3k
views
incorrect biomaRt output order of gene list
biomart ensembldb error
6.2 years ago Yuqia • 0
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
0
votes
3
replies
1.1k
views
Problem select / ensembl package
ensembldb
2.6 years ago yinnahm • 0
10
votes
18
replies
2.9k
views
ensembldb support for Ensembl's transcript_name column
ensembldb
updated 2.5 years ago by 16k • written 2.6 years ago by 42k
7
votes
6
replies
4.3k
views
Conversion of UniProt to Ensembl
biomaRt ensembldb UniProt.ws
updated 7 months ago by 700 • written 21 months ago by ▴ 20
2
votes
2
replies
1.3k
views
ensembldb and pseudogenes mapping to the same Ensembl ID
ensembldb
6.4 years ago meeta.mistry ▴ 30
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
2
votes
9
replies
2.4k
views
ensembldb salmon deseq2 txt2import right tool?
ensembldb deseq2
6.9 years ago aaron.dickey • 0
2
votes
3
replies
361
views
seqlevelsStyle() not working
ensembldb genomei GenomeInfoDb
3 months ago Kai Hu ▴ 70
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 ★ 2.0k • written 6.8 years ago by ★ 4.0k
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 ★ 2.0k • written 7.0 years ago by ▴ 660
3
votes
2
replies
1.6k
views
tximport with versioned identifiers
tximport ensembldb
6.6 years ago Ed Siefker ▴ 230
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
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 ★ 6.5k • written 2.6 years ago by • 0
5
votes
6
replies
2.5k
views
Is mapId supposed to concatenate multiVals?
annotationdbi ensembldb
updated 7.0 years ago by ★ 2.0k • written 7.0 years ago by ★ 13k
0
votes
1
reply
246
views
Canonical transcripts Mus musculus
TxDb.Mmusculus.UCSC.mm9.knownGene ensembldb GenomicFeatures Mus_musculus
updated 3 months ago by 65k • written 3 months ago by ▴ 10
6
votes
10
replies
2.3k
views
ensembldb: ensDbFromGtf error with ensembl version 74
ensembldb
updated 8.0 years ago by ★ 2.0k • written 8.0 years ago by ▴ 90
0
votes
2
replies
1.1k
views
ENSEMBL_MART_FUNCGEN not accessible through biomaRt?
biomart regulatory ensemble mart ensembldb
updated 7.9 years ago by ▴ 800 • written 7.9 years ago by ▴ 50
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 ★ 2.0k • written 7.9 years ago by ▴ 20
0
votes
3
replies
1.8k
views
errors with makeTxDbFromBiomart
biomart genomicfeatures maketxdbfrombiomart ensembldb ensDbFromGtf
updated 6.8 years ago by ★ 2.0k • written 6.8 years ago by • 0
3
votes
7
replies
3.1k
views
ensDbFromGtf error from gtf file downloaded from GENCODE.
ensembldb ensdbfromgtf
updated 6.7 years ago by ★ 2.0k • written 6.7 years ago by ▴ 40
1
vote
2
replies
1.3k
views
get_gene_transcript_exon_tables.pl extremely slow
ensembl ensembldb
updated 6.5 years ago by ★ 2.0k • written 6.5 years ago by ▴ 230
0
votes
5
replies
2.0k
views
error when using ensembldb with a MySQL server
ensembldb rmysql
updated 6.4 years ago by 65k • written 6.4 years ago by ▴ 10
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
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
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 ★ 2.0k • written 6.1 years ago by ▴ 100
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 ★ 2.0k • written 6.0 years ago by ▴ 30
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 65k • written 5.8 years ago by • 0
0
votes
1
reply
995
views
Pick coding vs non-coding from Ensembl data set
R ensembl ensembldb noncoding rna protein coding
updated 5.5 years ago by ★ 2.0k • written 5.5 years ago by • 0
4
votes
4
replies
2.7k
views
Retrieve canonical transcript for each gene via ensembldb R package
annotation ensembldb
updated 22 months ago by ▴ 40 • written 5.3 years ago by • 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 25k • written 4.2 years ago by ▴ 30
2
votes
1
reply
867
views
protein_domain_source from ensembldb and mapping with PFAM.db
ensembldb pfam.db
4.1 years ago bruce.moran ▴ 30
1
vote
1
reply
783
views
Is transcript color accessible through ensembldb? (gold = in both HAVANA+ENSEMBL)
ensembldb
updated 3.9 years ago by ★ 2.0k • written 3.9 years ago by ▴ 160
0
votes
4
replies
1.2k
views
Gene information (GRanges + sequence) to GenBank
granges genomic ranges genbankr ensembldb
updated 3.6 years ago by 65k • written 3.6 years ago by ▴ 20
1
vote
1
reply
1.3k
views
topGO question
Ensembl ensembldb
updated 3.5 years ago by 65k • written 3.5 years ago by • 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 ★ 2.0k • written 3.4 years ago by • 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
3
votes
1
reply
1.4k
views
Mouse to Human Genes using bioconductor
ensembldb
updated 9 months ago by 65k • written 9 months ago by ▴ 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 ★ 4.1k • written 2.4 years ago by • 0
1
vote
2
replies
1.1k
views
Unable to use ensembldb's "ensDbFromGff()" function on .gff file from NCBI
ensembldb RNASeq
3.1 years ago Torkel • 0
0
votes
1
reply
1.0k
views
bioMart Sscrofa_gene_ensembl getBM() paralogues ERROR
biomaRt ensembldb paralogues
updated 22 months ago by ★ 1.6k • written 22 months ago by • 0
2
votes
1
reply
1.5k
views
Retrieve gene description with ensembldb
biomaRt ensembldb AnnotationData
updated 3.1 years ago by ★ 2.0k • written 3.1 years ago by ▴ 510
0
votes
4
replies
1.1k
views
GO data for fgsea: should ensembl data be augmented to contain parent terms?
biomaRt GO ensembldb fgsea
19 months ago dario.beraldi • 0
2
votes
2
replies
1.1k
views
ensembldb to make the EnsDb for Human Version 105 using 'fetchTablesFromEnsembl' I'm on day two, can it be sped up?
ensembldb
2.2 years ago Matthew Thornton ▴ 360
50 results • Page 1 of 1
Recent ...
Replies
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: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
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?
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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