0
votes
1
reply
918
views
DESeq2 interaction between one continuous variable and one categorical variable
RNASeqData DESeq2
updated 2.1 years ago by ★ 13k • written 2.1 years ago by • 0
1
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3
replies
1.5k
views
FlowSOM Error in flowCore::read.FCS
FlowSOM
updated 2.1 years ago by ▴ 360 • written 2.1 years ago by • 0
1
vote
3
replies
1.1k
views
Pan-organism OrgDb database, Accession number translated to organism name in R
AccNo OrgDb convert Organismname RStudio
updated 2.1 years ago by 68k • written 2.1 years ago by • 0
1
vote
1
reply
853
views
gDNAx diagnostic output interpretation
gDNAx
updated 2.1 years ago by ▴ 40 • written 2.1 years ago by • 0
0
votes
1
reply
1.3k
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tximeta errors: couldn't find matching transcriptome, returning non-ranged SummarizedExperiment AND unable to find an inherited method for function '…
tximeta
updated 2.1 years ago by 43k • written 2.2 years ago by • 0
0
votes
2
replies
881
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Swimming downstream: transcript fold changes
DEXSeq stageR
2.1 years ago jbono ▴ 10
4
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9
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2.2k
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DESeq2 unable to handle large count values
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updated 14 months ago by 43k • written 2.1 years ago by • 0
0
votes
0
replies
954
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genomes
2.1 years ago JP Cartailler ▴ 40
0
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0
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Job: Bioinformatics Research Associate, Genomics and Genetics
genomes Genetics
2.1 years ago JP Cartailler ▴ 40
0
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2
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939
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Cannot open Sysmex Partec CUbe 6 .fcs with read.FCS
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2.1 years ago mrescan • 0
2
votes
5
replies
2.7k
views
SparseArray unable to install on Bioc 3.18
DESeq2 SummarizedExperiment SparseArray Install DelayedArray
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
votes
1
reply
845
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DESeq2 model for two genome system
RNASeq DESeq2
updated 2.1 years ago by 43k • written 2.2 years ago by • 0
0
votes
1
reply
924
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DESeq2: different results with and without releveling when providing contrast
DESeq2
updated 2.1 years ago by 43k • written 2.2 years ago by • 0
0
votes
1
reply
847
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Controling for Covariates With a Continuous Predictor Variable
Deseq DESeq2
updated 2.1 years ago by 43k • written 2.1 years ago by • 0
0
votes
2
replies
1.0k
views
Is my data too noisy for DESeq? Should I model noise as unwanted variation?
RNASeqData DESeq2
2.1 years ago Ben ▴ 10
0
votes
2
replies
1.4k
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TCGA counts to TPM from recount3 do not seem to right
recount3 TCGA RNASeq
updated 2.1 years ago by ★ 1.1k • written 2.2 years ago by ▴ 200
0
votes
0
replies
610
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nondetects and technical replicates
qPCR nondetects
2.1 years ago Ed Siefker ▴ 230
0
votes
2
replies
954
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SKAT-O method using GENESIS, question about range iterator using SeqVarWindowIterator
GENESIS SeqVarTools
updated 2.1 years ago by ▴ 890 • written 2.1 years ago by • 0
3
votes
1
reply
1.1k
views
read10xCounts for Cell Ranger 7 Output
DropletUtils
updated 2.1 years ago by ★ 5.0k • written 3.2 years ago by ★ 1.6k
1
vote
1
reply
1.2k
views
HOW to FIX - PCAir excludes all my SNPs because there is no chromosome information
GENESIS autosome-only=FALSE? PCAir
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 10
2
votes
4
replies
1.6k
views
Import a Bioconductor package that is only used in a vignette/.Rmd script
Bioconductor PackageType BiocStyle
updated 2.1 years ago by 4.2k • written 2.1 years ago by • 0
1
vote
4
replies
1.2k
views
rnaSeqGene workflow not available in Bioconductor 3.18
rnaseqGene Bioconductor3.18 DifferentialExpression release
updated 2.1 years ago by 43k • written 2.1 years ago by ▴ 60
0
votes
9
replies
3.3k
views
DESeq2 result really different when only use some sample vs all sample
deseq2 rnaseq
updated 2.1 years ago by • 0 • written 8.2 years ago by ▴ 60
4
votes
6
replies
3.7k
views
Conversion between different types of bioinformatic forms. (eg. NCBI protein to Ensembl protein) in R
RStudio convert ensembldb NCBI
updated 15 months ago by • 0 • written 2.2 years ago by • 0
0
votes
2
replies
2.7k
views
MA plot for DESEq2 analysis
RNASeqData DESeq2
2.1 years ago RHEA • 0
0
votes
0
replies
618
views
SGSeq how export PSI values for each typr of splice variant
SGSeq
2.1 years ago Alison • 0
1
vote
1
reply
615
views
DESeqResults object -> extract statistics results with rownames (gene)
DESeq2
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by ▴ 50
0
votes
2
replies
1.5k
views
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bioconductor artificialintelligence JobPosting machinelearning
written 2.3 years ago by 53k
0
votes
3
replies
1.4k
views
Support for installation and usage of TxDb.Hsapiens.UCSC.hg19.knownGene package in R version 4.2.2
Bioconductor BiocPkgTools
2.2 years ago • updated 2.1 years ago blessybo • 0
0
votes
7
replies
4.5k
views
Graphics API Version Mismatch Error with DESeq2 and ggplot2 in RStudio on Ubuntu 22.04
error RStudio ggplot2 DESeq2
updated 2.1 years ago by 68k • written 2.2 years ago by • 0
0
votes
3
replies
911
views
DESeq2: FPMs varying based on sample groups used
DESeq2
updated 2.1 years ago by ★ 5.0k • written 2.2 years ago by • 0
1
vote
4
replies
1.5k
views
controling for batch effect while preserving variation within repeated measures that unevenly distributed across batches
miRNA BatchEffect RNASeq limma
2.2 years ago Wending • 0
1
vote
1
reply
1.5k
views
Deploying to shinyapps.io returns error for BiocVersion and phangorn packages
BiocVersion phangorn ShinyApps
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
0
votes
0
replies
879
views
Gviz::GeneRegionTrack error with standard TxDb: "adding seqlevels to a TxDb object is not supported"
Gviz
2.2 years ago dbsgtk • 0
0
votes
8
replies
1.6k
views
Quickly calculating adjusted Fold Change with DESeq2
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2.2 years ago • updated 2.1 years ago Luca • 0
1
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0
replies
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Gviz : UcscTrack
rtracklayer UCSC Gviz
2.2 years ago yujin ▴ 10
0
votes
7
replies
4.0k
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Unable to install RefPlus - R=4.3.1, BiocManager=3.18
Install instal
updated 2.2 years ago by 68k • written 2.2 years ago by • 0
1
vote
1
reply
965
views
DEXSeq DEXSeqDataSet count matrix duplication
DEXSeq DRIMSeq DEXSeqDataSet columnduplication
2.2 years ago NiKo ▴ 10
0
votes
6
replies
1.4k
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Unable to replicate figures of CBCS data after nSolver and RUVSeq normalization
RUVSeq
updated 2.1 years ago by 43k • written 2.2 years ago by • 0
0
votes
0
replies
751
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Mfuzz package loading issues
Mfuzz MacBook loadingissues
2.2 years ago Jon • 0
0
votes
1
reply
680
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Advice needed on package using online databases (fails CHECK when database is down)
Bioconductor
updated 2.2 years ago by 4.2k • written 2.2 years ago by ▴ 30
0
votes
0
replies
872
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Include or exclude N/A genes (those without any KEGG annotation) when running Wilcox test?
KEGGREST KEGG RNASeq
2.2 years ago mch • 0
1
vote
3
replies
1.2k
views
Error in Gviz (actually, rtracklayer) | IdeogramTrack
rtracklayer Gviz
updated 2.2 years ago by 16k • written 2.2 years ago by ▴ 10
12
votes
10
replies
16k
views
biomaRt not working - lazy table error
error lazy R biomaRt table
updated 21 months ago by • 0 • written 2.2 years ago by ▴ 20
0
votes
4
replies
1.6k
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Mfuzz package loading issues
Mfuzz loadingissues macbook
2.2 years ago Jon • 0
0
votes
2
replies
873
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Can you help me generate a Bsgenome of the fusion genome of a human and HIV-1 virus?
BSgenome.Hsapiens.NCBI.GRCh38
2.2 years ago 13273976287 • 0
0
votes
1
reply
2.7k
views
Error when trying to create a heatmap with DESeq2
Heatmap RNA-seqanalysis heatmaps DESeq2
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by • 0
5
votes
2
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2.2k
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DecideTest vs topTAGs in edgeR
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updated 2.2 years ago by 53k • written 2.2 years ago by ▴ 10
0
votes
1
reply
1.3k
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How to calculate CDS start and End per transcript from GTF file
dNdScv GenomicFeatures TxDb
2.2 years ago rohitsatyam102 ▴ 20
2
votes
10
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Accounting for Batch effect reduces DEGs drastically
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2.2 years ago • updated 2.1 years ago rohitsatyam102 ▴ 20
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Error in SummarizedExperiment(assays = SimpleList(counts = countData)
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