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AnnotationHub
•
reset
0
votes
2
replies
175
views
AnnotationHub installation ‘Rcpp’ 1.0.6 is already loaded, but >= 1.0.7 is required
AnnotationHub
Install
updated 8 weeks ago by
shepherl
3.1k • written 8 weeks ago by
nhaus
• 0
0
votes
4
replies
177
views
AnnotationHub
AnnotationHub
9 weeks ago • updated 8 weeks ago
junliqilinpan
• 0
4
votes
6
replies
368
views
OrgDb (org.Hs.eg.db) missing many EntrezIDs and their Symbols (Compared to Ensembl GRChg8 v103)
AnnotationHub
OrganismDbi
org.Hs.eg.db
updated 10 weeks ago by
Gordon Smyth
45k • written 11 weeks ago by
Nathan
• 0
8
votes
9
replies
727
views
Where can I find EnsDb.Hsapiens.v105?
Ensembl
Rstudio
ensembldb
AnnotationHub
ensdb
updated 3 months ago by
Hervé Pagès
15k • written 3 months ago by
jon.klonowski
▴ 30
0
votes
2
replies
200
views
AnnotationHub problem
AnnotationHub
4 months ago
Jianxuan
• 0
4
votes
8
replies
530
views
Problem converting transcript to genomic coordinates with Annotation Hub
AnnotationHub
5 months ago • updated 6 days ago
nattzy94
▴ 20
1
vote
3
replies
364
views
How delete the AnnotationHub downloaded datasets
AnnotationHub
updated 7 months ago by
Mike Smith
★ 5.5k • written 7 months ago by
sabermohammdi.1994
• 0
2
votes
10
replies
744
views
Getting Bioconductor genome wide annotation for Candida auris
AnnotationFilter
annotationTools
AnnotationHub
AnnotationData
updated 7 months ago by
Guido Hooiveld
★ 3.2k • written 7 months ago by
Javan Okendo
• 0
0
votes
0
replies
158
views
LRBaseDbi error
LRBaseDbi
AnnotationHub
8 months ago
Francois Marchildon
▴ 20
1
vote
2
replies
416
views
Translating Solanum lycopersum gene IDs to ENTREZIDs for GO enrichment analysis using clusterProfiler
OrgDb
Bioconductor
AnnotationHub
clusterProfiler
updated 12 months ago by
Guido Hooiveld
★ 3.2k • written 12 months ago by
ju.ry
• 0
0
votes
1
reply
388
views
News:
Updates to BiocFileCache, AnnotationHub, and ExperimentHub
BiocFileCache
AnnotationHub
ExperimentHub
cache
13 months ago
shepherl
3.1k
0
votes
2
replies
1.2k
views
Convert Agilent Probe ID to gene IDs/Symbols
AnnotationHub
biomaRt
14 months ago
rohitsatyam102
▴ 20
3
votes
8
replies
1.6k
views
GO enrichment analysis on Solanum lycopersicum proteomics dataset (UniProt IDs)
clusterProfiler
AnnotationHub
GO
uniprot
updated 8 weeks ago by
Guido Hooiveld
★ 3.2k • written 15 months ago by
Alberto
• 0
11
votes
13
replies
1.1k
views
How to retrieve genomic coordinates for a list of entrezID and their respective gene names
genomic
AnnotationHub
GenomicRanges
org.Hs.eg.db
18 months ago • updated 15 months ago
rohitsatyam102
▴ 20
8
votes
20
replies
10k
views
ah <- AnnotationHub() Error in UseMethod("filter_"): no applicable method for 'filter_' applied to an object of class "c('tbl_SQLiteConnection', 'tb…
AnnotationHub
dplyr
18 months ago • updated 10 months ago
georgia.katsoula
▴ 40
3
votes
2
replies
835
views
Issue with AnnotationHub
AnnotationHub
17 months ago
rahnaman
▴ 10
1
vote
2
replies
390
views
How to mimic biomaRt results with AnnotationHub?
biomaRt
AnnotationHub
18 months ago
Ezgi
▴ 30
1
vote
3
replies
346
views
AnnotationHub: failed to load resource name
AnnotationHub
20 months ago
ben.ponv
• 0
4
votes
17
replies
1.0k
views
annotation conversion from old microarray to latest Entrez and Ensembl ID
biomaRt
annotation
Ensembl
annotationHub
updated 20 months ago by
Kevin Blighe
3.5k • written 20 months ago by
Didi
▴ 10
4
votes
2
replies
534
views
News:
ensembldb EnsDb databases for Ensembl release 101 added to AnnotationHub
EnsDb
ensembldb
annotation
AnnotationHub
News
21 months ago
Johannes Rainer
★ 1.9k
8
votes
16
replies
1.7k
views
Cannot connect to ExperimentHub server
ExperimentHub
AnnotationHub
SingleR
updated 21 months ago by
shepherl
3.1k • written 21 months ago by
enricoferrero
▴ 610
0
votes
2
replies
377
views
Can't select GO from AnnotationHub orgDB packages
GO.db
AnnotationHub
OrgDB
updated 22 months ago by
James W. MacDonald
59k • written 22 months ago by
Jenny Drnevich
★ 2.0k
0
votes
3
replies
360
views
extracting the genes associated with a specific pathway
pathway
KEGG
annotation
annotationhub
updated 23 months ago by
James W. MacDonald
59k • written 23 months ago by
Bogdan
▴ 640
2
votes
4
replies
533
views
How to manage AnnotationHub snapshots / most OrgDB are missing?
AnnotationHub
OrgDb
snapshotDate
updated 2.0 years ago by
shepherl
3.1k • written 2.0 years ago by
Jenny Drnevich
★ 2.0k
2
votes
8
replies
518
views
gene enrichment using enrichGO function throuth annotationHub orgDb
software error
enrichGO
annotationHub
clusterProfiler
Job
updated 2.1 years ago by
James W. MacDonald
59k • written 2.1 years ago by
bnajafpour
• 0
1
vote
5
replies
393
views
AnnotationHub; Error: failed to load resource; Timeout was reached: [annotationhub.bioconductor.org]
annotationhub
updated 2.1 years ago by
shepherl
3.1k • written 2.1 years ago by
dilaik
• 0
0
votes
2
replies
286
views
hg38 tracks for AnnotationHub
annotationhub
2.2 years ago
Michael Love
37k
0
votes
1
reply
289
views
AnnotationHub display() gives JavaScript Alert and DataTables warning
AnnotationHub
Shiny
Rstudio
updated 2.2 years ago by
shepherl
3.1k • written 2.2 years ago by
bwiley4
• 0
0
votes
8
replies
1.0k
views
I can't use AnnotationHub()
AnnotationHub
2.4 years ago
755606975
• 0
1
vote
3
replies
1.2k
views
AnnotationHub timeout for Ensembl Mouse GTF
AnnotationHub
Ensembl
Mouse
AnnotationHub Ensembl
2.4 years ago
dmgatti
▴ 10
3
votes
0
replies
393
views
News:
EnsDb databases for Ensembl release 98 provide now also transcripts' GC content
annotation
ensembldb
EnsDb
AnnotationHub
News
2.5 years ago
Johannes Rainer
★ 1.9k
0
votes
2
replies
514
views
how to choose annotation file in AnnotationHub web server
annotation
AnnotationHub
2.5 years ago
15958021290
▴ 10
3
votes
4
replies
456
views
Are AH52264, AH66175, and AH70594 duplicates?
AnnotationHub
updated 2.6 years ago by
shepherl
3.1k • written 2.6 years ago by
Aditya
▴ 140
1
vote
3
replies
382
views
Problem with AnnotationHub after crash during first download of metadata
AnnotationHub
updated 2.7 years ago by
shepherl
3.1k • written 2.8 years ago by
konstantinos.bogias
▴ 10
7
votes
44
replies
1.9k
views
OrgDB download failed via AnnotationHub
annotationhub
orgdb
updated 2.9 years ago by
shepherl
3.1k • written 2.9 years ago by
chirag.parsania
• 0
2
votes
0
replies
415
views
News:
ensembl 96 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
updated 3.0 years ago by
nguyenlieuduoc
• 0 • written 3.1 years ago by
shepherl
3.1k
1
vote
4
replies
468
views
AnnotationHub Server denied you to change the given directory
annotation
annotationhub
updated 3.0 years ago by
shepherl
3.1k • written 3.0 years ago by
bastien.ducreux
▴ 10
0
votes
11
replies
804
views
AH134 and other AnnotationHub objects unavailable as "defunct"
AnnotationHub
updated 3.1 years ago by
shepherl
3.1k • written 3.1 years ago by
Robert K. Bradley
▴ 40
1
vote
1
reply
472
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
3.1 years ago
wecai
• 0
3
votes
9
replies
2.8k
views
AnnotationHub corrupt database
annotationhub
updated 3.2 years ago by
shepherl
3.1k • written 6.8 years ago by
Koen Van den Berge
▴ 180
0
votes
0
replies
485
views
News:
ensembl 95 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
annotationdata
ensembl
gtf
2bit
News
3.3 years ago
shepherl
3.1k
5
votes
12
replies
1.3k
views
Ensembl plants at annotationHub?
ensembl
ensembldb
plant
arabidopsis thaliana
annotationhub
updated 6 days ago by
Johannes Rainer
★ 1.9k • written 3.5 years ago by
Guido Hooiveld
★ 3.2k
1
vote
7
replies
585
views
News:
ensembl 94 gtfs and fasta twobits have been added to AnnotationHub
annotationdata
annotationhub
ensembl
gtf
2bit
News
3.6 years ago
shepherl
3.1k
0
votes
5
replies
586
views
annotationhub: data update
annotationhub
updated 3.8 years ago by
shepherl
3.1k • written 3.8 years ago by
Kasper Daniel Hansen
6.5k
0
votes
0
replies
521
views
News:
ensembl 93 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
ensembl
gtf
2bit
annotationdata
News
3.8 years ago
shepherl
3.1k
1
vote
2
replies
879
views
AnnotationHub, force update snapshot date?
annotationhub
updated 3.9 years ago by
shepherl
3.1k • written 3.9 years ago by
Vang Le
▴ 70
5
votes
4
replies
784
views
Eliminating repetitive calls to ExperimentHub
experimenthub
annotationhub
large dataset
4.0 years ago
slinker
▴ 20
0
votes
6
replies
781
views
initialization of AnnotationHub() in version 2.12.0 is problematically verbose
AnnotationHub
updated 4.0 years ago by
Martin Morgan
25k • written 4.0 years ago by
Robert K. Bradley
▴ 40
0
votes
0
replies
603
views
News:
ensembl 92 gtfs and fasta twobits have been added to AnnotationHub
ensembl
gtf
2bit
annotationhub
News
4.1 years ago
shepherl
3.1k
1
vote
0
replies
1.0k
views
News:
ensembl 91 gtfs and fasta twobits have been added to AnnotationHub
annotationhub
ensembl
gtf
2bit
News
4.4 years ago
shepherl
3.1k
50 results • Page
1 of 1
Recent ...
Replies
Comment: Transcript-level differential expression using DESeq2
by
Ekta
• 0
Ok.. thanks for your valuable suggestion and quick replies. I have generated an MA plot using plotMASwish. thanks ekta
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2
by
Michael Love
37k
Sorry, I haven't seen this. Maybe try filtering low count genes? ``` keep <- rowSums(counts(dds) >= 10) >= X dds <- dds[keep,] # then run …
Comment: Transcript-level differential expression using DESeq2
by
Michael Love
37k
To show some extent of the DTE you can plot the LFC of the significant set and their mean count, we have `plotMASwish` to do this. Another…
Comment: Transcript-level differential expression using DESeq2
by
Ekta
• 0
No, the Volcano plot is not essential. I just wanted to show DETs with the help of a plot. Could you suggest a way for it? What are the oth…
Comment: Warnings when using "ashr" in lfcshrinkage for DESeq2
by
andrebolerbarros
▴ 10
Hi Michael, I'm using the "contrast" parameter, so I cannot use apeglm with that, as far as I know. The "coef" will not allow me to do eve…
Votes
Comment: Transcript-level differential expression using DESeq2
Comment: Transcript-level differential expression using DESeq2
Answer: how to make a group to apply the data to CAMERA
Answer: how to make a group to apply the data to CAMERA
Comment: Using vegan::betadisper for determing if I subset my design for DESeq2
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59k
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3.5k
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