0
votes
3
replies
931
views
Strange patterns in Log2fold change output
DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
votes
0
replies
1.1k
views
flowjo_to_gatingset function error
CytoML
4.9 years ago Iman • 0
0
votes
0
replies
1.3k
views
Fitzig function in MetagenomeSeq package
metagenomeSeq fitzig
4.9 years ago Andrew • 0
1
vote
1
reply
1.0k
views
Accounting for fish body mass in DE?
GeneExpression edgeR
updated 4.9 years ago by 68k • written 4.9 years ago by • 0
1
vote
1
reply
2.1k
views
DiffBind error with background=TRUE in dba.normalize?
BiocParallel DiffBind parallel
updated 4.9 years ago by ★ 5.2k • written 4.9 years ago by • 0
2
votes
2
replies
1.6k
views
Design formula for pairwise comparison of experimental setup with multiple factors
DEGs DESeq2
4.9 years ago 2021yearsold • 0
0
votes
1
reply
1.5k
views
DESeq2 - shrunken LFC calculation
apeglm DESeq2
updated 4.9 years ago by 43k • written 4.9 years ago by ▴ 50
2
votes
2
replies
4.9k
views
mapping gene type or biotype to ENSEMBL ID
ensembldb biomaRt org.Hs.eg.db Annotation
updated 4.9 years ago by ★ 2.1k • written 4.9 years ago by • 0
1
vote
7
replies
2.7k
views
Weird results after lfc command (shrinkage)
lfcshrinkage DESeq2
updated 4.9 years ago by 43k • written 5.0 years ago by • 0
8
votes
20
replies
6.8k
views
Using DiffBind blacklists and greylists with results mapped to BDGP6
DiffBind
updated 3.9 years ago by ★ 5.2k • written 5.0 years ago by ▴ 10
0
votes
4
replies
3.8k
views
Bam files causing Blacklist errors in dba.analyze() but not in dba.blacklist()
DiffBind
5.0 years ago • updated 4.9 years ago ahua217 ▴ 10
0
votes
1
reply
668
views
DESeq2 paired design with missing samples
missingdata DESeq2 paired-sample
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
1
vote
1
reply
1.5k
views
addPatternDensity in 'qsea' takes too much time
MBD-seq qsea BiocParallel
updated 4.9 years ago by ▴ 280 • written 5.0 years ago by • 0
5
votes
5
replies
5.2k
views
Issues with installation status of R package rtracklayer
rtracklayer Bioconductor
updated 3.8 years ago by 4.2k • written 5.0 years ago by ▴ 840
2
votes
8
replies
4.2k
views
How to remove X & Y chromosome genes from RNAseq data
DESeq2 RNASeq
updated 24 months ago by • 0 • written 5.0 years ago by ▴ 20
4
votes
4
replies
1.2k
views
Something strange in the ranking of genes by DESeq2
DESeq2
5.0 years ago Dejian Zhao ▴ 10
0
votes
2
replies
3.7k
views
Error with package clusterProfiler: "Error in abs(stats) : non-numeric argument to mathematical function"
Bioconductor BIOCOND clusterProfiler
updated 3.5 years ago by • 0 • written 5.0 years ago by • 0
0
votes
12
replies
8.2k
views
ChAMP input: Beta Matrix?
champ dmr analysis
updated 17 months ago by • 0 • written 9.8 years ago by • 0
0
votes
3
replies
2.1k
views
Help on sapply() with GRanges
updated 5.0 years ago by • 0 • written 12.1 years ago by ▴ 260
1
vote
1
reply
1.5k
views
Differential exon usage analysis using DEXSeq for mRNA and lncRNA separately
DEXSeq
updated 5.0 years ago by ★ 1.9k • written 5.0 years ago by • 0
0
votes
0
replies
601
views
Unique K number set or all K number set?
clusterProfiler
5.0 years ago XM • 0
12
votes
2
replies
2.1k
views
`TxDb.Hsapiens.UCSC.hg19.knownGene` and `EnsDb.Hsapiens.v75` can't be installed anymore
EnsDb.Hsapiens.v75 TxDb.Hsapiens.UCSC.hg19.knownGene
5.0 years ago Batool ▴ 370
2
votes
6
replies
5.2k
views
Package not available for R.4.0.2
R.4.0.2 tissueGeneExpression
updated 5.0 years ago by • 0 • written 5.2 years ago by • 0
0
votes
3
replies
1.8k
views
Using transformed matrix in DESeq2
DESeq2 VST
updated 5.0 years ago by ★ 5.0k • written 5.0 years ago by • 0
0
votes
0
replies
1.5k
views
Using IlluminaHumanMethylation450kanno.ilmn12.hg19 and froze at installation.
IlluminaHumanMethylation450kanno.ilmn12.hg19
5.0 years ago whirlsyu • 0
2
votes
3
replies
11k
views
DESeq2: Multiple Comparisons with Different Conditions and Replicates
Interactions DESeq2 Design
updated 4.9 years ago by ★ 4.0k • written 5.0 years ago by ▴ 30
4
votes
6
replies
3.1k
views
Extract canonical coding sequence with getBM
Bioconductor biomaRt
5.0 years ago heiko_kin ▴ 60
0
votes
4
replies
2.0k
views
GO.db package can't be installed
install GO.db
updated 5.0 years ago by 25k • written 5.0 years ago by • 0
18
votes
4
replies
2.6k
views
`ggbio` package can't be loaded
ggbio
5.0 years ago • updated 4.9 years ago Batool ▴ 370
6
votes
8
replies
3.6k
views
Interaction with DESeq2 via DiffBind
diffbind deseq2 interactions
updated 5.0 years ago by • 0 • written 8.1 years ago by ▴ 60
0
votes
0
replies
1.5k
views
Job: Computational Biologist at Denali Therapeutics
Transcriptomics SingleCell JobPosting
5.0 years ago Steve Lianoglou ★ 13k
14
votes
1
reply
2.7k
views
it paused in line **byte-compile and prepare package for lazy loading** when install package EnsDb.Hsapiens.v75
EnsDb.Hsapiens.v75
updated 5.0 years ago by ▴ 370 • written 5.0 years ago by ▴ 70
3
votes
7
replies
4.4k
views
Error when loading DEP in RStudio
dep
updated 4.9 years ago by ▴ 10 • written 5.3 years ago by ▴ 20
1
vote
1
reply
2.1k
views
Limma-Voom - Time series experiment with one group (duplicateCorrelation() function)
voom duplicateCorrelation() timeseries limma
updated 5.0 years ago by 53k • written 5.0 years ago by ▴ 10
0
votes
0
replies
1.1k
views
flow cytometry differential expression through time
cytofWorkflow cytof diffcyt
5.0 years ago achaillon • 0
0
votes
0
replies
854
views
CytofWorkflow and automate the classification of cellular sub-populations
cytofWorkflow
5.0 years ago achaillon • 0
0
votes
1
reply
2.5k
views
Install using BiocManager::install() doesn't work in docker container
Bioconductor docker Install
updated 5.0 years ago by 25k • written 5.0 years ago by • 0
0
votes
1
reply
1.2k
views
Matrix not full rank (time-series experiment with one group and covariates )
DESeq2 DES
updated 5.0 years ago by 43k • written 5.0 years ago by ▴ 10
2
votes
4
replies
2.3k
views
read.idat function misleading error when reading compressed files
idat illumina limma read.idat
updated 5.0 years ago by 53k • written 5.0 years ago by • 0
2
votes
1
reply
2.4k
views
DESeq usage of transcript TPM after tximport
tximport
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
0
votes
0
replies
1.5k
views
Job: Proteomics Bioinformatician
JobPosting Proteomics Statistics Job
5.0 years ago Laura • 0
1
vote
1
reply
1.1k
views
DESeq2 interactions genotype condition code needed
DESeq2 anova condition genotypeeval
updated 5.0 years ago by ★ 5.0k • written 5.0 years ago by ▴ 20
5
votes
10
replies
2.9k
views
Learning DiffBind - some basic questions
DiffBind
updated 4.8 years ago by ★ 5.2k • written 5.0 years ago by ▴ 10
2
votes
1
reply
1.3k
views
Bewildering PCA plot at DiffBind
DiffBind
updated 5.0 years ago by ★ 5.2k • written 5.0 years ago by ▴ 10
0
votes
7
replies
2.8k
views
Error while running DE in DESeq2
DESeq2
updated 4.2 years ago by • 0 • written 5.0 years ago by • 0
0
votes
1
reply
1.7k
views
Trouble with Tximport
Taeniopygia_guttata_Data RnaSeqSampleSize
updated 5.0 years ago by ★ 5.0k • written 5.0 years ago by • 0
2
votes
6
replies
9.5k
views
color scale in cnetplot (enrichplot) is not centered in 0, skewed towards positive values
enrichplot clusterProfiler
5.0 years ago • updated 4.9 years ago Emilia ▴ 40
1
vote
8
replies
4.8k
views
Problem selectively labelling points in the Enhanced Volcano package
EnhancedVolcano
5.0 years ago Peter ▴ 10
2
votes
3
replies
3.0k
views
Selecting or not selecting samples before running GSVA
GSVA
updated 5.0 years ago by ★ 3.4k • written 5.0 years ago by ▴ 20
1
vote
1
reply
1.4k
views
Which group is meant by greater oder less in the gage results?
gage
updated 5.0 years ago by ★ 1.6k • written 5.0 years ago by ▴ 20
46,695 results • Page 140 of 934
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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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