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Author footnotes in BiocWorkflowTools::f1000_article template
BiocWorkflowTools
rmarkdown
5.6 years ago
helucro
▴ 70
0
votes
1
reply
1.6k
views
DESeq2: error message
deseq2
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
whyw6948
• 0
0
votes
5
replies
1.3k
views
DEseq2 2x2 design using a grouping variable
deseq2
~group
5.6 years ago
weichengz
▴ 10
1
vote
7
replies
1.2k
views
Extracting results for a single chromosome
deseq2
5.6 years ago
Charlotte
• 0
3
votes
10
replies
2.3k
views
CRISPRseek OffTargetAnalysis Warning: Error in Hash and NAs introduced by coercion
CRISPRseek
Error in hash
NAs introduced by coercion
updated 5.6 years ago by
Julie Zhu
★ 4.3k • written 5.6 years ago by
nils.hassel
• 0
0
votes
2
replies
679
views
How to perform contrasts within groups
deseq2
5.6 years ago
Charlotte
• 0
0
votes
1
reply
982
views
Problem with installing the package ph525x
ph525x
updated 5.6 years ago by
shepherl
4.2k • written 5.6 years ago by
sadegheh.haghshenas
• 0
0
votes
1
reply
1.3k
views
the function DMR in ChAMP package
ChAMP
DMR
updated 5.6 years ago by
Yuan Tian
▴ 290 • written 5.6 years ago by
olive8306
• 0
0
votes
0
replies
1.3k
views
reactomePA error input file
r
reactomePA
enrichment
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
camillab.
▴ 10
0
votes
1
reply
1.4k
views
blosc compression with rhdf5
rhdf5
updated 5.6 years ago by
Mike Smith
★ 6.6k • written 5.6 years ago by
hoganajjunk+bioc
• 0
4
votes
2
replies
2.3k
views
Limma: how to interpret logFC for interaction contrast
limma
logFC
factor interaction
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
Natalia
• 0
0
votes
1
reply
2.9k
views
GO vs GOALL in rrvgo and GOSemSim
rrvgo
GOSemSim
GO.db
5.6 years ago
Jenny Drnevich
★ 2.0k
8
votes
7
replies
3.1k
views
readMSData and netCDF files, how to set polarity ?
MSnbase
updated 5.6 years ago by
Johannes Rainer
★ 2.1k • written 5.6 years ago by
julien.kermorvant
▴ 30
1
vote
4
replies
5.5k
views
Non-integer values in salmon counts change DE analyses
deseq2
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
mlosada323
• 0
0
votes
3
replies
1.7k
views
extracting the genes associated with a specific pathway
pathway
KEGG
annotation
annotationhub
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
Bogdan
▴ 670
0
votes
0
replies
1.2k
views
News:
Bioc2020 - Virtual Conference Registration
bioc2020
conference
registration
News
5.6 years ago
shepherl
4.2k
0
votes
0
replies
1.1k
views
News:
Updated annotation packages
annotation
news
News
5.6 years ago
kayla.interdonato
▴ 160
4
votes
1
reply
4.2k
views
News:
Nominations for Bioconductor Awards!
Bioc2020
Bioconductor
Awards
Recognition
News
5.7 years ago • updated 5.6 years ago
shepherl
4.2k
0
votes
3
replies
616
views
Determining sample size in contrast groups
deseq2
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
jacob.westaway
• 0
4
votes
2
replies
1.2k
views
edgeR Time course analysis, choice on degree of freedom
edger
updated 5.6 years ago by
Gordon Smyth
53k • written 5.6 years ago by
Ruixuan
▴ 10
6
votes
6
replies
2.0k
views
Suggestion for next revision of edgeR User Guide re Design matrix setup
edger
error
updated 5.6 years ago by
Gordon Smyth
53k • written 5.6 years ago by
pdunn
• 0
4
votes
14
replies
2.4k
views
Application of quantro to RNASeq: I do not get the same results as are in the quantro paper supplement
quantro
RNASeq
updated 5.6 years ago by
Stephanie Hicks
▴ 80 • written 5.7 years ago by
raf4
▴ 30
3
votes
2
replies
12k
views
Error from DegPlot $<-.data.frame`(`*tmp*`, "xs", value = integer(0)) : replacement has 0 rows, data has 96
DEGreport
DegPlot
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
kavator
▴ 30
0
votes
3
replies
2.4k
views
What is the use of the BStringSet?
BioStrings
BStringSet
StringSet
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
skigirl618
• 0
2
votes
1
reply
1.8k
views
Cross-species analysis and normalization with DESeq2
normalization
deseq2
across species
rnaseq
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
rmurray2050
• 0
1
vote
0
replies
957
views
Understanding ColData in BiSeq
BiSeq
Coldata
5.6 years ago
akhaira
• 0
0
votes
1
reply
1.3k
views
namespace conflict flowAI and ggCyto
software error
flow cytometry
ggcyto
flowAI
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
Robert Baer
▴ 70
0
votes
6
replies
2.0k
views
DESeq2 log2foldchange shows opposite sign than clearly visible in pseudocounts or vst values (correct order in contrast)
deseq2
log2FoldChange
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
ligia.mateiu
• 0
4
votes
8
replies
3.5k
views
Don't let TopGo to trimm long GO names
go
software error
topgo
rna-seq
updated 2.9 years ago by
James W. MacDonald
68k • written 5.6 years ago by
morteza.aslanzadeh
▴ 30
1
vote
3
replies
905
views
Differential gene expression analysis
deseq2
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
DataFanatic
▴ 10
1
vote
0
replies
1.4k
views
Job:
Post-Doctoral Research Fellow, Cancer Genomics
genomics
seattle
bioinformatics
data science
statistics
Job
5.6 years ago
Fred Hutch (Recruiting)
▴ 40
1
vote
0
replies
1.4k
views
Job:
Post-Doctoral Research Fellow, Biostatistics - Seattle, WA
BIOSTATISTICS
SEATTLE
WASHINGTON
COMPUTATIONAL BIOLOGY
Job
5.6 years ago
Fred Hutch (Recruiting)
▴ 40
0
votes
7
replies
2.9k
views
DESeq error: Error in validityMethod(object) : nrow(design) == ncol(object) is not TRUE
deseq2
DESeq
nrow == ncol is not TRUE
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
maniermk
• 0
1
vote
6
replies
1.4k
views
Rescaling predictors in DESeq changes outcomes?
deseq2
glm
rescale
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
jc.szamosi
▴ 10
5
votes
4
replies
2.6k
views
ggcyto wrong axis scale?
ggcyto
flowWorkspace
flow cytometry
flowjo
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 5.6 years ago by
andrej.stoll.de
▴ 10
2
votes
7
replies
9.0k
views
Error wth Installation BiocManager
software error
updated 3.9 years ago by
weiran
• 0 • written 5.6 years ago by
hasmikmd
▴ 10
1
vote
1
reply
1.8k
views
clusterProfiler merge_result dotplot
clusterProfiler
updated 4.7 years ago by
jodi.thomas
• 0 • written 5.6 years ago by
Giovanni Calice
▴ 160
0
votes
1
reply
926
views
EBTest error please add gene/isoform names to the data matrix
EBSeq
5.6 years ago
lli2
• 0
0
votes
1
reply
1.2k
views
Argument map.symbol converting IDs even when its value is FALSE
pathview
updated 5.6 years ago by
Kevin Blighe
★ 4.0k • written 6.8 years ago by
arthur.vinx
• 0
0
votes
1
reply
1.4k
views
Difficulty Installing Bioconductor
Installation
updated 5.6 years ago by
Martin Morgan
25k • written 5.6 years ago by
terrylthomas2804
• 0
0
votes
3
replies
1.8k
views
DESeq2: Subset dataset or use interaction in design
deseq2
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
jeffsheng
• 0
1
vote
2
replies
2.4k
views
Help installing clusterProfiler
clusterProfiler
DO.db
GO.db
lazy load fail
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
masaver
• 0
0
votes
2
replies
1.3k
views
Problem in dowloading "TxDb.Hsapiens.UCSC.hg38.knownGene"
annotation
software
TxDb
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
AmalAbdel-Aziz
• 0
0
votes
2
replies
1.1k
views
openCyto Problem: Registered Gating Function Executes Twice when Called
openCyto
register_plugins
gs_add_gating_method
5.6 years ago
geoffreylewen
• 0
0
votes
1
reply
2.3k
views
GSVA on integrated/batch corrected scRNAseq data
GSVA
Job
updated 5.6 years ago by
Robert Castelo
★ 3.4k • written 5.6 years ago by
laura.derooij
• 0
0
votes
0
replies
1.0k
views
News:
Single Package Builder / New Package Submission
new package
build machines
infrastructure
News
5.6 years ago
shepherl
4.2k
2
votes
7
replies
1.9k
views
Affycoretools package, HTA 2.0 annotation for non-coding RNA
affy
rna
hta2.0
r
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
Marco_aurelio
• 0
0
votes
3
replies
2.1k
views
Strange p values for DEG analysis with covariates using DESeq2
deseq2
edgeR
salmon
tximport
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
iaradsouza1
• 0
0
votes
2
replies
1.1k
views
rnaseqDTU Workflow, Precision estimation error.
rnaseqDTU
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
dixit.anirudha
• 0
0
votes
6
replies
821
views
How to treat genes in RNAseq analyses
deseq2
updated 5.6 years ago by
James W. MacDonald
68k • written 5.6 years ago by
mlosada323
• 0
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I totally feel you on the struggle to manage package versions! Just last month, I had to roll back a package in R for a project because the…
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