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Annotationhub
•
reset
11
votes
13
replies
4.0k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic
AnnotationHub
GenomicRanges
org.Hs.eg.db
3.4 years ago • updated 3.2 years ago
rohitsatyam102
▴ 20
9
votes
11
replies
5.7k
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 5 weeks ago by
shepherl
3.8k • written 2.2 years ago by
jon.klonowski
▴ 40
9
votes
21
replies
15k
views
ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tb…
AnnotationHub
dplyr
updated 20 months ago by
SmallChess
▴ 10 • written 3.4 years ago by
georgia.katsoula
▴ 40
8
votes
4
replies
4.4k
views
Tutorial:
Epigenomics RoadMap Project files now accessible via AnnotationHub
AnnotationHub
Epigenomics
BigData
RoadMap Project
NIH
Tutorial
updated 7.0 years ago by
vanesa_1230
• 0 • written 8.9 years ago by
Sonali Arora
▴ 390
8
votes
16
replies
6.1k
views
Cannot connect to ExperimentHub server
ExperimentHub
AnnotationHub
SingleR
updated 3.7 years ago by
shepherl
3.8k • written 3.7 years ago by
enricoferrero
▴ 660
7
votes
44
replies
5.4k
views
OrgDB download failed via AnnotationHub
annotationhub
orgdb
updated 4.8 years ago by
shepherl
3.8k • written 4.8 years ago by
chirag.parsania
• 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
cagenet34
▴ 20 • written 8.1 years ago by
Rinaldo Bertossa
▴ 20
7
votes
36
replies
5.5k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 15 days ago by
Shiva
• 0 • written 5.4 years ago by
Guido Hooiveld
★ 3.9k
6
votes
9
replies
4.5k
views
BiocFileCache/ExperimentHub/AnnotationHub temporary ERROR
BiocFileCache
AnnotationHub
ExperimentHub
updated 5 weeks ago by
Melissa
• 0 • written 5 months ago by
shepherl
3.8k
5
votes
2
replies
1.2k
views
AnnotationHub: two broad peaks from same url are not the same
annotationhub
bugs
encode
bed
7.4 years ago
wcstcyx
▴ 30
5
votes
4
replies
1.3k
views
Eliminating repetitive calls to ExperimentHub
experimenthub
annotationhub
large dataset
5.9 years ago
slinker
▴ 20
5
votes
11
replies
2.5k
views
Certificate problem with ExperimentHub / AnnotationHub
software error
curatedmetagenomicdata
annotationhub
experimenthub
updated 7.3 years ago by
Levi Waldron
★ 1.1k • written 7.3 years ago by
morganx
▴ 10
4
votes
3
replies
1.9k
views
Error installing AnnotationHub on Fedora
Annotationhub
curl
httr
fedora
updated 7.9 years ago by
anastazie.d
▴ 30 • written 8.6 years ago by
barashe
▴ 10
4
votes
8
replies
1.8k
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
2.4 years ago • updated 23 months ago
nattzy94
▴ 20
4
votes
17
replies
2.4k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt
annotation
Ensembl
annotationHub
updated 3.6 years ago by
Kevin Blighe
★ 3.9k • written 3.6 years ago by
Didi
▴ 10
4
votes
7
replies
1.6k
views
AnnotationHub and ExperimentHub make "~" directory in my home
annotationhub
experimenthub
updated 7.6 years ago by
Valerie Obenchain
★ 6.8k • written 7.6 years ago by
Michael Love
41k
4
votes
10
replies
1.2k
views
Suggestion: spinning wheel for AnnotationHub
annotationhub
updated 6.6 years ago by
shepherl
3.8k • written 6.7 years ago by
Michael Love
41k
4
votes
1
reply
3.7k
views
getting the longest transcript by gene from Refseq
refseq
annotationhub
updated 8.6 years ago by
Martin Morgan
25k • written 8.6 years ago by
dalloliogm
▴ 50
4
votes
2
replies
1.6k
views
News:
ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb
ensembldb
annotation
AnnotationHub
News
3.6 years ago
Johannes Rainer
★ 2.0k
4
votes
6
replies
2.2k
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub
OrganismDbi
org.Hs.eg.db
updated 2.1 years ago by
Gordon Smyth
50k • written 2.1 years ago by
Nathan
• 0
3
votes
3
replies
1.4k
views
Broken AnnotationHub resource (AH25517 | wgEncodeOpenChromDnaseGm12878Pk.narrowPeak.gz)
annotationhub
encode
updated 8.1 years ago by
Valerie Obenchain
★ 6.8k • written 8.1 years ago by
Peter Hickey
▴ 740
3
votes
4
replies
1.1k
views
Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 4.5 years ago by
shepherl
3.8k • written 4.5 years ago by
Aditya
▴ 160
3
votes
13
replies
2.6k
views
Org.db: why a supposed unique key (ID) has multiple entries?
annotationhub
organismdb
orgdb
unsupported organisms
updated 8.2 years ago by
Valerie Obenchain
★ 6.8k • written 8.2 years ago by
Guido Hooiveld
★ 3.9k
3
votes
4
replies
1.1k
views
Annotation hub and clusterProfiler errors
clusterProfiler
Annotationhub
updated 5 months ago by
Guido Hooiveld
★ 3.9k • written 5 months ago by
BS
• 0
3
votes
2
replies
2.0k
views
Issue with AnnotationHub
AnnotationHub
3.4 years ago
rahnaman
▴ 10
3
votes
9
replies
4.0k
views
AnnotationHub corrupt database
annotationhub
updated 5.1 years ago by
shepherl
3.8k • written 8.7 years ago by
Koen Van den Berge
▴ 180
3
votes
11
replies
4.9k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 10 weeks ago by
Guido Hooiveld
★ 3.9k • written 3.2 years ago by
Alberto
• 0
3
votes
2
replies
1.6k
views
AnnotationHub: A RPKM data.frame of Epigenomics RoadMap Project seems strange
annotationhub
roadmap project
rpkm
data.frame
7.5 years ago
wcstcyx
▴ 30
3
votes
6
replies
2.2k
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub
OrgDb
snapshotDate
updated 21 months ago by
shepherl
3.8k • written 3.9 years ago by
Jenny Drnevich
★ 2.0k
3
votes
0
replies
1.0k
views
News:
EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation
ensembldb
EnsDb
AnnotationHub
News
4.4 years ago
Johannes Rainer
★ 2.0k
3
votes
1
reply
1.3k
views
AnnotationHub: confusing pValue/qValue for (some) Roadmap records
roadmap project
annotationhub
epigenomics
big data
updated 8.0 years ago by
Valerie Obenchain
★ 6.8k • written 8.0 years ago by
kevin.rue
▴ 350
2
votes
2
replies
1.9k
views
Normal Patient Samples from GSE62944
GSE62944
annotationhub
differentialexpression
updated 8.1 years ago by
Sonali Arora
▴ 390 • written 8.1 years ago by
hamda.binte.ajmal
• 0
2
votes
2
replies
1.2k
views
how to choose annotation file in AnnotationHub web server
annotation
AnnotationHub
4.4 years ago
15958021290
▴ 10
2
votes
1
reply
311
views
clusterProfiler, AnnotationHub, and discrepancies in GO Terms
Atlanticsalmon
clusterPro
Salmosalar
AnnotationHub
GeneOntology
updated 7 weeks ago by
Michael Love
41k • written 7 weeks ago by
Filipe
• 0
2
votes
8
replies
1.7k
views
Problem fetching resources from AnnotationHub, error 403
AnnotationHub
updated 8.4 years ago by
Valerie Obenchain
★ 6.8k • written 8.5 years ago by
Johannes Rainer
★ 2.0k
2
votes
0
replies
969
views
News:
ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
updated 4.9 years ago by
nguyenlieuduoc
• 0 • written 5.0 years ago by
shepherl
3.8k
2
votes
0
replies
3.3k
views
News:
Gencode GFF3 and FASTA files now available via AnnotationHub
AnnotationHub
Gencode
GFF3
FASTA
News
8.6 years ago
Sonali Arora
▴ 390
2
votes
12
replies
2.3k
views
AnnotationHub-cant extract database
annotationhub
updated 7.0 years ago by
Valerie Obenchain
★ 6.8k • written 7.0 years ago by
ecpierce
• 0
2
votes
10
replies
2.3k
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter
annotationTools
AnnotationHub
AnnotationData
updated 2.5 years ago by
Guido Hooiveld
★ 3.9k • written 2.5 years ago by
Javan Okendo
• 0
2
votes
28
replies
4.3k
views
Problem making orgdb package for bacteria (Pseudomonas) using annotation hub and annotation forge
AnnotationHub
AnnotationForge
Pseudomonas_aeruginosa
updated 4 months ago by
James W. MacDonald
65k • written 16 months ago by
Manmohit
▴ 10
2
votes
3
replies
1.3k
views
Why No Uniprot information for some other organisms in AnnotationHub?
hub
annotationhub
updated 3.2 years ago by
shepherl
3.8k • written 7.6 years ago by
wssdandan2009
• 0
2
votes
12
replies
3.1k
views
Error: failed to load 'AnnotationHub' resource
biomart
annotationhub
updated 8.4 years ago by
Martin Morgan
25k • written 8.4 years ago by
borowczak.marc
▴ 10
2
votes
6
replies
1.4k
views
R getting "stuck" with RoadMap resource retrieval through AnnotationHub
roadmap project
annotationhub
7.0 years ago
vanesa_1230
• 0
2
votes
0
replies
860
views
News:
ensembl 89 gtfs and fasta twobits have been added to AnnotationHub
bioconductor
annotationhub
ensembl89
News
6.9 years ago
shepherl
3.8k
2
votes
8
replies
1.6k
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error
enrichGO
annotationHub
clusterProfiler
Job
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
bnajafpour
• 0
2
votes
2
replies
748
views
[BigWigFile] import as RLE vs default and length comparaison
BSgenome.Hsapiens.UCSC.hg19
rtracklayer
AnnotationHub
20 months ago • updated 19 months ago
Lenny186
• 0
1
vote
3
replies
3.5k
views
Problem using display() function on RStudio
display
rstudio
annotationhub
updated 8.6 years ago by
James W. MacDonald
65k • written 8.6 years ago by
barashe
▴ 10
1
vote
4
replies
1.2k
views
AnnotationHub Server denied you to change the given directory
annotation
annotationhub
updated 5.0 years ago by
shepherl
3.8k • written 5.0 years ago by
bastien.ducreux
▴ 10
1
vote
3
replies
2.1k
views
annotation of SV (Structural Variants)
variantannotation
annotationhub
7.1 years ago
Bogdan
▴ 670
1
vote
1
reply
1.0k
views
The total genes items (e.g. ENTREZ ID, SYMBOL) in OrgDb (Salmo salar; [["AH66207"]]) is just half the gene number in NCBI ?!
Annotationhub
Annotationdb
profiler
annotationdbi
5.0 years ago
wecai
• 0
50 results • Page
1 of 1
Recent ...
Replies
Comment: Which input file is used for DGEList in EgdeR?
by
i.atanasoai
• 0
Understood, Thank you very much for the reply, very kind.
Comment: Which input file is used for DGEList in EgdeR?
by
Michael Love
41k
"gene_counts_length_scaled.tsv file generated by the nf-core be exactly that?" No that is the counts scaled by the length. Counts + offset…
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa
by
Michael Love
41k
These genes are fine. They are just the ones where, by chance, the sample variance is below the sample mean. It happens. DESeq2 brings thes…
Comment: DEG with low counts
by
Michael Love
41k
These counts are too low, only a few samples above a count of 10. So for typical RNA-seq data that is underpowered to call differences. It…
Comment: DESeq filtering specific to contrasts
by
Michael Love
41k
If the counts are too low it in one group then you can't make the comparison either way (whether they are filtered out or just under-powere…
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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