1
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1
reply
922
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Can I run deseq2 on two separate experiments at once?
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updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
4
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8
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2.8k
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DESEQ2 - What is the recommended workflow in terms of pre-filtering and counts normalization?
DESeq2 Transcriptomics
updated 2.7 years ago by ★ 13k • written 2.7 years ago by ▴ 20
1
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Job: Research Assistant - Computational Biology/Immunology, Memorial Sloan Kettering, New York
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2.7 years ago Chrysothemis ▴ 10
0
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3
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How to correctly interpret ALDEx2 output - differential abundance testing
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updated 2.7 years ago by • 0 • written 3.0 years ago by • 0
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Decidetest results summary different from results written as .csv file
edgeR voom decidetests DEG
updated 2.7 years ago by 53k • written 2.7 years ago by • 0
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3
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How to import dataset from other software into DESeq2?
DESeq2
updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by • 0
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974
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WGCNA approach on multiregional brain transcriptomes
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2.7 years ago Levi • 0
2
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3
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RNA-seq analysis without replicates
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updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
0
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1
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675
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Can a expressed gene dataset yielded after CPM be used in DESeq2 and EdgeR?
DESeq2 edgeR
updated 2.7 years ago by ★ 4.1k • written 2.7 years ago by • 0
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8
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Interpreting ellipses in PCAtools for bulk RNAseq
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updated 2.7 years ago by • 0 • written 4.5 years ago by • 0
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1
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511
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DESeq
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updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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3
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BiomaRt: problems annotating a list of DEGs from DESeq2
biomaRt
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
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2
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1.4k
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ggplot and geom_lines for clustering
ggplot
updated 2.7 years ago by ▴ 90 • written 2.7 years ago by • 0
3
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6
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1.6k
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Mistake in Cook's distance calculation in DESeq2 or am I missing something?
DESeq2
2.7 years ago phil.xie • 0
5
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8
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1.9k
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Help with error install csaw
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written 2.7 years ago by ▴ 20
1
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1
reply
959
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Add 'ColSideColors' using 'heatmap.2' function
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updated 2.7 years ago by ▴ 90 • written 2.7 years ago by ▴ 10
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2
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734
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Inverted log2foldchange in study?
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updated 2.7 years ago by ▴ 90 • written 2.7 years ago by • 0
1
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3
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how to add an enrichment score to a kegg pathway enrichment analysis?
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updated 2.7 years ago by ★ 4.1k • written 2.7 years ago by ▴ 10
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1
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699
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DESeq2 statistical model construction
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updated 2.7 years ago by ★ 1.4k • written 2.7 years ago by ▴ 20
0
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399
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How to set dropout rate using splatSimDropout function of splatter ?
lazappi
2.7 years ago shamsuzzaman86 • 0
0
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0
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757
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Estimating factors of unwanted variation for DTU analysis
RUVSeq DRIMSeq
2.7 years ago Luca • 0
0
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0
replies
1.1k
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Confusing DSS outputs with smoothing (DMLtest)
DSS
2.7 years ago Weisheng • 0
3
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5
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1.6k
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How to annotate genes from results of DiffBind
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updated 2.6 years ago by 68k • written 2.7 years ago by ▴ 20
0
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2
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2.5k
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Access Ensembl GRCH38 Version 87 Using BiomaRt
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updated 2.7 years ago by ★ 2.1k • written 2.7 years ago by • 0
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4
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Error with regionCounts()
csaw
2.7 years ago Chris ▴ 20
0
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3
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DRIMseq error for paired sample analysis
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2.7 years ago Luca • 0
0
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1
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1.0k
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How to get around the warning message: mzR has been built against a different Rcpp version
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updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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2
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RNA-Seq normalization of pre and post treatment groups
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0
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1
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908
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Error in names(label_color[label_color == "organe"]) <- "lysosome" : 'names' attribute [1] must be the same length as the vector [0]
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updated 2.7 years ago by ▴ 40 • written 2.7 years ago by • 0
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2
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RPPA data (Proteomics analysis)
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2.7 years ago • updated 2.6 years ago qiz218591 • 0
0
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2
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Full list of differential genes not obtained in topTable
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updated 2.7 years ago by 53k • written 2.7 years ago by • 0
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LmFit error in EPIC methylation array analysis, Minfi
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updated 2.7 years ago by 53k • written 2.7 years ago by • 0
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AnnotationDbi Error: PROSITE is defunct.
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2.7 years ago ahiser • 0
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3
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*** caught segfault *** , cause 'memory not mapped'
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updated 2.7 years ago by 68k • written 2.7 years ago by • 0
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array CGH software
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2
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Scaling and normalization by deconvolution of SMART-Seq 2 data
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2.7 years ago Assa Yeroslaviz ★ 1.5k
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13
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Help with Error in DiffBind
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2.7 years ago Chris ▴ 20
0
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0
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600
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Best practice for comparing a subset of data /
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2.7 years ago TzuChiao ▴ 10
1
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6
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can negative value microarray matrix data analysed by limma directly
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updated 2.3 years ago by 53k • written 5.2 years ago by ▴ 20
5
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15
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how can I do gene differential analysis on data after vst
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written 2.7 years ago by ▴ 20
1
vote
2
replies
985
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Performing DE analysis using edgeR for PhIP-seq data with multiple samples, some with some without replicates.
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2.7 years ago f_rahmdani • 0
2
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4
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2.7k
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Failed to install Biobase
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updated 2.7 years ago by 68k • written 2.7 years ago by • 0
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3
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Annotated dendogram (tree) from tbl_graph
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2.7 years ago christian.dina • 0
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2
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pathview: Warning: Failed to download KEGG xml/png files, hsa04110 skipped!
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2.7 years ago 덕윤 • 0
0
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0
replies
951
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Using a clustree object to draw a "classical" dendogram
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2.7 years ago christian.dina • 0
0
votes
1
reply
776
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HiCDCPlus extract_hic_eigenvectors() only works with larger bin sizes (> =250kb )?
HiCDCPlus
updated 2.5 years ago by • 0 • written 2.7 years ago by • 0
2
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2
replies
1.3k
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Latest version of ggtree (3.6.2) unavailable on Anaconda. Only 3.6.0 exists.
ggtree
updated 17 months ago by • 0 • written 2.7 years ago by ▴ 10
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2
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1.4k
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Multiple issues reading in peak sets with Diffbind
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updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by • 0
1
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1
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1.1k
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HISAT2 mapping
hisat2 results
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
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Reducing dataset size to improve run time for fitGAM in tradeSeq
tradeSeq pseudotime
updated 2.7 years ago by ▴ 180 • written 3.0 years ago by • 0
46,692 results • Page 56 of 934
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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…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
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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