Showing : AnnotationDbi • reset
19
votes
6
replies
35k
views
How to map all Ensembl IDs to Gene Symbols- Problem with AnootationDbi
rnaseq annotationdbi
updated 7.6 years ago by ★ 6.8k • written 7.6 years ago by ▴ 70
13
votes
12
replies
6.5k
views
From a ENST to ENSG
AnnotationDbi
3.2 years ago suxxa ▴ 20
9
votes
2
replies
2.4k
views
How to deal with Affymetrix GeneChip probeids that map to multiple genes
hta20sttranscriptcluster.db probe mapping annotation pd.hta.2.0 annotationdbi
updated 7.6 years ago by 65k • written 7.6 years ago by ▴ 20
8
votes
12
replies
3.9k
views
How to create tx2gene data.frame when there's no TxDb object for the organism you are working with.
tximport deseq2 annotationdbi
updated 6.6 years ago by ★ 2.0k • written 6.6 years ago by • 0
7
votes
11
replies
6.4k
views
Error in sqliteSendQuery(conn, statement): error in statement: no such table: c.probes
edgeR limma annotationhub kegga annotationdbi
updated 7.8 years ago by ▴ 20 • written 8.1 years ago by ▴ 20
6
votes
1
reply
6.3k
views
Finding orthologous human/mouse ENSEMBL IDs
human mouse ensembl annotationdbi homologue
6.9 years ago Keith Hughitt ▴ 180
6
votes
6
replies
2.2k
views
Weird output of biomaRt R package querying Ensembl IDs (hg19/grch37) to retrieve gene symbols
biomaRt annnotation RNASeq AnnotationDbi
2.9 years ago svlachavas ▴ 830
5
votes
7
replies
1.3k
views
Concatenation of Bimap
AnnotationDbi Concatenate
updated 8.4 years ago by 65k • written 8.4 years ago by ★ 1.5k
5
votes
3
replies
3.7k
views
Is it possible to annotated mitochondrial genes with ENSEMBL ids and Homo.sapiens/Mus.musculus?
homo.sapiens annotationdbi
updated 6.4 years ago by ★ 2.0k • written 6.4 years ago by ▴ 40
5
votes
22
replies
5.5k
views
sqliteSendQuery error in AnnotationForge bioconductor package
bioconductor annotationforge annotationdbi annotation r
updated 7.8 years ago by ★ 1.0k • written 9.2 years ago by • 0
5
votes
7
replies
2.5k
views
Duplicated ENTREZID gene annotations org.Hs.eg.db
ENTREZID SYMBOL AnnotationDbi org.Hs.eg.db
updated 3.3 years ago by 50k • written 3.3 years ago by • 0
5
votes
6
replies
2.5k
views
Is mapId supposed to concatenate multiVals?
annotationdbi ensembldb
updated 6.9 years ago by ★ 2.0k • written 6.9 years ago by ★ 13k
5
votes
11
replies
1.6k
views
an error in BioMart regarding gene annotations
biomart AnnotationDbi
updated 5.8 years ago by ▴ 50 • written 5.8 years ago by ▴ 670
5
votes
11
replies
1.6k
views
Inconsistent data within org.Sc.sgd.db package
org.Sc.sgd.db AnnotationDbi
updated 2.2 years ago by • 0 • written 4.2 years ago by • 0
4
votes
1
reply
1.7k
views
Retrieving all genes related a go term
go R annotationdbi biomart
updated 6.6 years ago by 65k • written 6.6 years ago by ▴ 40
4
votes
5
replies
1.5k
views
Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens.UCSC.hg19.knownGene
ensembl cdschrom org.Hs.eg.db AnnotationDbi SingleCellExperiment
updated 5.1 years ago by 65k • written 5.1 years ago by ▴ 10
4
votes
8
replies
4.4k
views
Annotating DEseq output using AnnotationDbi mapIds and most results say NA
AnnotationDbi mapIds org.Mm.eg.db ENSEMBLTRANS
updated 7.3 years ago by 65k • written 7.3 years ago by ▴ 10
4
votes
2
replies
1.8k
views
mapIds to get GO terms
annotationdbi go.db
updated 8.4 years ago by 25k • written 8.4 years ago by ▴ 10
4
votes
4
replies
1.9k
views
Annotation with org.Hs.eg.db Genome Build 38
AnnotationDbi org.Hs.eg.db
3.4 years ago Bine ▴ 40
4
votes
3
replies
2.2k
views
Gene conversion from SYMBOL to ENTREZ using AnnotationDbi doesn't convert some of the genes
AnnotationDbi org.Hs.eg.db
3.4 years ago Emilia ▴ 30
4
votes
2
replies
1.4k
views
ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
AnnotationDbi EnsDb.Hsapiens org.Hs.eg.db
updated 3.3 years ago by ★ 2.0k • written 3.3 years ago by • 0
4
votes
5
replies
1.9k
views
makeOrgPackage - ERROR: Two fields in the source DB have the same name
software error AnnotationForge AnnotationDbi
updated 4.0 years ago by 65k • written 4.0 years ago by • 0
3
votes
1
reply
1.2k
views
[PrimeView] Affymetrix Human Gene Expression Array
AnnotationDbi [PrimeView]AffymetrixHumanGeneExpressionArray
updated 2.8 years ago by ★ 3.9k • written 2.8 years ago by • 0
3
votes
6
replies
2.8k
views
Problem with annotating ENSEMBLE IDs to GENE SYMBOL with AnnotationDBI mapIDs
annotation ensembl annotationdbi
5.8 years ago vd4mmind • 0
3
votes
4
replies
1.9k
views
DGE matrix annotation
DGE DESeq2 AnnotationDbi
updated 5.6 years ago by 65k • written 5.6 years ago by • 0
3
votes
3
replies
2.4k
views
Get the latest gene name from Entrez ID
AnnotationDbi org.Hs.eg.db
3.1 years ago sgupt46 • 0
3
votes
5
replies
1.7k
views
Selecting few ids from reactome.db
annotationdbi reactome.db bug
updated 7.4 years ago by 25k • written 7.4 years ago by ▴ 730
3
votes
5
replies
1.7k
views
GO.db installation fails (MacOS, AnnotationDbi, R3.5.0)
GO bioclite R3.5 mac os x annotationdbi
updated 5.9 years ago by 25k • written 5.9 years ago by ▴ 30
3
votes
3
replies
5.0k
views
failing to install the package org.Hs.eg.db in R (version 3.5.2 )
org.Hs.eg.db AnnotationDbi
updated 14 months ago by • 0 • written 5.2 years ago by • 0
3
votes
2
replies
951
views
select With Regular Expression
annotationdbi Wildcard
updated 7.8 years ago by ★ 2.0k • written 7.8 years ago by ★ 1.5k
3
votes
2
replies
1.9k
views
how to use select() to retrieve GO Biological Process Ancestors?
GO.db AnnotationDbi
updated 3.2 years ago by 25k • written 3.2 years ago by ★ 3.9k
3
votes
18
replies
2.8k
views
Annotating codelink data file
r codelink annotation annotationdbi
updated 9.0 years ago by ▴ 760 • written 9.0 years ago by ▴ 260
3
votes
2
replies
2.5k
views
Mapping Ensemble IDs with version numbers using ensembl annotation packages
AnnotationDbi ensembldb
3.2 years ago Ezgi ▴ 60
3
votes
2
replies
1.5k
views
Trouble getting probe ID info from mouse4302.db annotation package with a specific RefSeq ID.
annotationdbi mouse4302 affymetrixchip annotationdata R
updated 8.4 years ago by 65k • written 8.4 years ago by • 0
3
votes
1
reply
2.1k
views
Converting between UCSC id and gene symbol with bioconductor annotation resources
AnnotationData AnnotationDbi annotation
updated 2.6 years ago by 65k • written 2.6 years ago by • 0
3
votes
5
replies
3.0k
views
Map TxDb.Hsapiens.UCSC.hg19.knownGene TXID keys to ENSEMBL transcript ID or Refseq ID
annotationdbi
updated 7.4 years ago by 65k • written 7.4 years ago by ▴ 10
2
votes
3
replies
1.6k
views
Get MANE transcripts from TxDb.Hsapiens.UCSC.hg38.knownGene
AnnotationDbi
updated 8 months ago by 65k • written 23 months ago by ▴ 30
2
votes
17
replies
986
views
Problem installing package, version of dependency issue
AnnotationDbi GO.db
updated 3 months ago by ▴ 730 • written 3 months ago by ▴ 50
2
votes
2
replies
3.4k
views
problem using AnnotationDbi
annotationdbi bioconductor
6.2 years ago h72ghorashi • 0
2
votes
5
replies
1.7k
views
Get corresponding gene id for probe id from Affymetrix array
AnnotationDbi Microarray
23 months ago nhaus ▴ 30
2
votes
3
replies
1.2k
views
org.Hs.eg.db gives more than one ENTREZID for a gene symbol
org.Hs.eg.db AnnotationDbi
updated 15 months ago by 65k • written 15 months ago by • 0
2
votes
5
replies
1.6k
views
building a new annotation
Annotation AnnBuilder AnnotationDbi Annotation AnnBuilder AnnotationDbi
updated 15.1 years ago by ★ 7.2k • written 15.1 years ago by ▴ 10
2
votes
1
reply
1.8k
views
Missing SYMBOL keytype in EnsDb.Hsapiens.v75
annotationdbi EnsDb.Hsapiens.v75
updated 7.7 years ago by ★ 2.0k • written 7.7 years ago by ▴ 10
2
votes
3
replies
1.7k
views
Gene Ontology Analysis of DE Genes
clusterProfiler AnnotationDbi OrgDb goseq
updated 3.2 years ago by 65k • written 3.2 years ago by ▴ 30
2
votes
3
replies
2.0k
views
Convert Refseq Protein IDs to UniProt IDs
AnnotationDbi
3.4 years ago sgupt46 • 0
2
votes
1
reply
3.9k
views
Find correct annotation for specific agilent platforms Whole Human Genome Microarray 4x44K
agilent whole Human Genome Microarray 4X44K annotationdbi bioconductor
8.5 years ago Konstantinos Yeles ▴ 80
2
votes
3
replies
2.7k
views
org.Mm.eg.db mm9 version for ChIPpeakAnno getEnrichedGO function
chippeakanno annotationdbi
updated 6.5 years ago by • 0 • written 8.5 years ago by • 0
2
votes
2
replies
1.8k
views
Cannot retrieve Annotations for a GENEID from Homo.sapiens
annotation annotationdbi homo.sapiens
updated 9.5 years ago by 65k • written 9.5 years ago by ▴ 50
2
votes
4
replies
2.3k
views
Problems during the installation of AnnotationDbi and pasilla
AnnotationDbi
updated 9.5 years ago by ▴ 200 • written 9.5 years ago by • 0
2
votes
3
replies
2.0k
views
tximport::summarizeToGene fails to ignoreTxVersion
tximport tximeta AnnotationDbi
4.8 years ago Benjamin • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge by shuwangxinze1996 • 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio by Kevin Blighe ★ 3.9k
I am not sure how your comment helps here?
Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k
> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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