1
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4
replies
2.6k
views
merge TPM values for same geneID
RNASeqRData TPM
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by ▴ 10
2
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2
replies
1.3k
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BAMBU extended gtf file?
BAMBU bambu
updated 3.2 years ago by • 0 • written 3.3 years ago by ▴ 10
1
vote
1
reply
1.0k
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Bambu data loading issue
BAMBU bambu
updated 3.3 years ago by ▴ 20 • written 3.3 years ago by ▴ 10
1
vote
9
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4.6k
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DEGreport installation help
DEGreport
updated 2.4 years ago by 68k • written 3.3 years ago by ▴ 20
2
votes
3
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4.0k
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GSEA only returning 1 GO term - unable to map Ensembl IDs with decimals?
AnnotationDbi GO clusterProfiler enrichplot ensembldb
updated 3.3 years ago by ▴ 150 • written 3.3 years ago by ▴ 10
1
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2
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1.2k
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" 'end' must be >= 'start' - 1" error in cn.mops
cn.mops
3.3 years ago User000 • 0
0
votes
3
replies
1.7k
views
CountOverlap
GeneExpression ChIPSeqData
updated 3.3 years ago by 68k • written 3.3 years ago by ▴ 20
3
votes
7
replies
3.1k
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Different results between Limma and DESEQ2 for Differential Expression Analysis
DESeq2 limma
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by ▴ 50
0
votes
2
replies
1.8k
views
color scale ggcyto::autoplot
ggcyto
3.3 years ago alex • 0
1
vote
0
replies
1.5k
views
adjusted p-values with topGO elim.KS method
topGO Ontology DifferentialExpression
3.3 years ago Kevin Gregory ▴ 10
0
votes
3
replies
1.3k
views
expression data
ExpressionData ExpressionNormalizationWorkflow
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
2
votes
9
replies
2.9k
views
Error when plotting flow cytometry data
FlowCytometry flowCore ggcyto
updated 3.3 years ago by ▴ 360 • written 3.3 years ago by • 0
0
votes
1
reply
2.8k
views
Treeplot by enrichplot
clusterProfiler enrichplot treeplot
updated 3.2 years ago by ★ 1.2k • written 3.3 years ago by • 0
0
votes
0
replies
970
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question on the p value for VIPER results by dorothea
RNAseq VIPER Doth
3.3 years ago snowmattin • 0
5
votes
8
replies
3.1k
views
Question on performing filtering by gene expression on a normalized matrix in limma?
expression R filtering limma
3.3 years ago • updated 3.1 years ago mohammedtoufiq91 ▴ 10
0
votes
0
replies
984
views
Outliers
Proteomics Proteome
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
0
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0
replies
1.6k
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HISAT2 and HTSEQ command
HTSeqGenie
3.3 years ago Maryam.sed1400 • 0
2
votes
2
replies
983
views
Error when run scCATCH
scCATCH
3.3 years ago Chris ▴ 20
0
votes
4
replies
6.9k
views
Understanding the Log2FoldChange calculated with DESeq2 and according to formula log2(treated/control)
DESeq2 log2FC
3.3 years ago User000 • 0
1
vote
2
replies
2.7k
views
transcripts missing from tx2gene
tximport
3.3 years ago Erick • 0
0
votes
0
replies
1.3k
views
WCGNA: Using Eigengenes when correlating modules to external features? What about PC2, PC3???
Network Transcriptomics MicrobiomeData RNASEQ WCGNA
3.3 years ago Julieta • 0
0
votes
1
reply
981
views
Annotation data packages for plant parasitic nematodes
AnnotationData Annotation
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
3
votes
5
replies
2.0k
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DESEQ2 several samples per individual
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 50
0
votes
1
reply
1.4k
views
Comparison between treatment timepoints in a single timeseries (control is first timepoint)
DESeq2 single-timeseries TimeSeriesExperiment
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
votes
1
reply
1.0k
views
Design Matrix Singularity Error
DES DESIGN
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
votes
1
reply
1.2k
views
Set up "mock" cell type as the reference?
DESeq2 SingleCell
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
1
vote
1
reply
945
views
Contrasts in Deseq2
DESeq2
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
votes
1
reply
1.1k
views
tximport: not all(file.exists(files)) are true
tximport
updated 3.3 years ago by 43k • written 3.3 years ago by • 0
0
votes
5
replies
3.3k
views
Outlier gene counts either killing or driving DEGs with DESeq2. PLEASE HELP.
DESeq2 DEG
3.3 years ago • updated 3.2 years ago marinaw ▴ 20
0
votes
2
replies
1.9k
views
How to fix warning in makeTxDbFromGFF() when using Gencode M30 (mouse)?
GenomicFeatures AnnotationHubData tximeta
updated 3.3 years ago by 43k • written 3.3 years ago by ▴ 10
0
votes
1
reply
909
views
interaction term formula for DESEQ2?
DESeq2
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by • 0
0
votes
1
reply
547
views
Bioconductor Rpackages install
DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
1
vote
6
replies
2.4k
views
How to annotate Data with oligo and Affymetrix HuGene-2_0-st package?
oligo
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
2
votes
1
reply
1.3k
views
WGCNA: weird issue of module with a single gene
network co-expression WGCNA
updated 3.3 years ago by ▴ 50 • written 3.3 years ago by ▴ 10
0
votes
2
replies
1.3k
views
Cannot install TxDb.Athaliana.BioMart.plantsmart51
TxDb.Athaliana.BioMart.plantsmart51
updated 3.3 years ago by 16k • written 3.3 years ago by ▴ 30
1
vote
2
replies
893
views
Do we need to correct any of the data from DESeq2, if we only want to investigate some of the comparisons?
DESeq2 correction
3.3 years ago smac_head • 0
0
votes
1
reply
1.2k
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
TreeSummarizedExperiment phylogenetic microbiome SummarizedExperiment
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
2
votes
4
replies
1.7k
views
Error message from protein coding prediction with VariantAnnotation
R VariantAnnotation
3.3 years ago rwan.work • 0
1
vote
4
replies
2.0k
views
QSEA: choose appropriate reference for TMM normalisation with qsea::addLibraryFactors / qsea::estimateLibraryFactors
TMM edgeR qsea MEDIPS
updated 3.3 years ago by • 0 • written 3.3 years ago by ▴ 20
0
votes
0
replies
922
views
weighting sample group
monocle SingleCell DifferentialExpression
3.3 years ago Sogand • 0
0
votes
1
reply
1.1k
views
Missing a list of ensembl gene dataset for some species
biomaRt
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
0
votes
0
replies
1.4k
views
Simplify - clusterProfiler
RNASeq simplify clusterProfiler enrichGO simplifyEnrichment
3.3 years ago estafana.t98 • 0
0
votes
0
replies
1.4k
views
Job: Postdoctoral research scientist in computational biology/statistical genetics/functional genomics at Columbia University, USA
Alzheimer's StatisticalMethod Genetics molecularQTL FunctionalGenomics
3.3 years ago gaow • 0
0
votes
3
replies
2.3k
views
Generate Heatmap from Gene Names after DESEQ2
DESeq2 DESEQ2 tximeta SummarizedExperiment heatmaps
updated 3.3 years ago by 68k • written 3.3 years ago by • 0
0
votes
1
reply
1.2k
views
tcga expression data
TCGAWorkflow
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
2
votes
2
replies
1.4k
views
Gene abundance DESEq
DESeq2
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
0
votes
11
replies
2.4k
views
limma::contrast.fit() potential bugs when weights from voom() included
bugs limma
3.3 years ago Zhenyu • 0
3
votes
1
reply
4.3k
views
Understanding tximport working with salmon outputs
Transcriptomics tximport
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by ▴ 10
1
vote
3
replies
2.0k
views
Clarification about DESeq2 counts() function when dealing with covariates
DESeq2
updated 3.3 years ago by ★ 1.4k • written 3.3 years ago by • 0
1
vote
3
replies
1.9k
views
rtacklayer::import.bed silently adds 1 to the start coordinates
rtracklayer
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by ▴ 30
46,712 results • Page 76 of 935
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