4
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6
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2.1k
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Speedglm dependency issue?
nullranges
2.6 years ago Kathleen Reed ▴ 20
0
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1
reply
1.0k
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Can't make a boxplot or hist with oligo
oligo
updated 2.6 years ago by 68k • written 2.7 years ago by • 0
1
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2
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Error in getCdfInfo(object) :
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2.6 years ago kobra • 0
0
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0
replies
716
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Cannot generate plots when calling ChAMP
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2.6 years ago Kan • 0
0
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0
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602
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Gene A mutation vs Gene B amplification using TCGA datasets
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2.6 years ago Begin-R • 0
2
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4
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2.6k
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How to get TPM / FPKM after batch correction with DESeq2?
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2.6 years ago vk • 0
0
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0
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847
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Reading FCS files using read.FCS
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2.7 years ago Pilid • 0
0
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1
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764
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Sample expression calculation in rna seq
Rnaseq
updated 2.6 years ago by ★ 5.0k • written 2.7 years ago by • 0
0
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0
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856
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topGO: how do I retrieve my genes contributing to the GO term enrichment
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2.7 years ago Priya • 0
9
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16
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3.0k
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How to apply ChIPpeakAnno to your Granger object to annotate the peaks?
ChIPpeakAnno
2.7 years ago • updated 2.6 years ago Chris ▴ 20
2
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3
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1.5k
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Using gcrma() and using the t-test to compare single genes of interest for disease vs healthy comparison?
gcrma CustomCDF Affyhgu133aExpr limma affy
updated 2.6 years ago by 68k • written 2.7 years ago by ▴ 10
0
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2
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1.3k
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error in champ.SVD
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updated 2.7 years ago by 4.2k • written 2.7 years ago by • 0
2
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2
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Error in checkFullRank(modelMatrix)
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updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 30
1
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2
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1.8k
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Filter by expression and keep probes in limma
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2.7 years ago Abdul ▴ 20
1
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1
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3.2k
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FPKM t-test vs DEseq2
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updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by ▴ 10
0
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1
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1.2k
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EGSEA::egsea - Parallelization issue and "Error in array(col.rgb[, i], dim(node.rgb)[3:1]) : negative length vectors are not allowed"
egsea EGSEA123
2.7 years ago • updated 2.6 years ago neilzhao ▴ 30
0
votes
1
reply
868
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Can I use baseMean (from DESeq2) as part of presenting/ interpreting results
DESeq2 diferentialabundance 16srRNA baseMean
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
0
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4
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1.0k
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Down weighing an outlier in DESeq2 ?
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updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
0
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0
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1.3k
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Job: Bioinformatics postdoc position at Penn State University
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2.7 years ago yuzun • 0
0
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2
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1.5k
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How to find the number of protein-coding genes in each chromosome arm in human?
gene chromosome proteincodinggene
2.7 years ago Liliian • 0
0
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0
replies
939
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Are LFQ workflow arguments from DEP package all required or optional?
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2.7 years ago aymanreffai • 0
2
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0
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2.6k
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How to aggregate pseudobulks: Normalization & Log-Transformation
pseudobulk scRNAseq GSVA
2.7 years ago Tadeoye ▴ 20
1
vote
1
reply
851
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Performing a one-sided test for differential expression analysis in edgeR
edgeR
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
0
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0
replies
970
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Manually adjusting BCV for exactTest in edgeR based on plotBCV
edgeR
2.7 years ago f_rahmdani • 0
1
vote
1
reply
3.3k
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Error with Pathview: Bad Request (HTTP 400)
KEGGREST pathview R
updated 2.7 years ago by ★ 4.1k • written 2.7 years ago by ▴ 10
4
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5
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3.6k
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EnhancedVolcano - Unable to customize the length of Connectors to Gene Labels
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updated 2.7 years ago by ★ 4.0k • written 2.7 years ago by ▴ 20
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4
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Unable to install BiocManager
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updated 2.7 years ago by ▴ 50 • written 2.7 years ago by • 0
6
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6
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DESeq2 for single cell pseudobulk processing
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updated 2.6 years ago by 43k • written 2.7 years ago by ▴ 10
0
votes
1
reply
564
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Package requires binary executable from external software?
external executable
updated 2.6 years ago by ★ 5.0k • written 2.7 years ago by • 0
0
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0
replies
822
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How to extract the counts for non-split reads from paired end RNA-seq data?
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2.7 years ago barrypraveen • 0
0
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1
reply
776
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Differential express genes in one group across all time points
DESeq2 edgeR BP4RNAseq ensemblVEP
updated 2.7 years ago by 43k • written 2.7 years ago by • 0
4
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5
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Adding cell population estimates as a covariate in DESeq2 differential gene expression analysis
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updated 18 months ago by • 0 • written 2.7 years ago by ▴ 10
0
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3
replies
1.7k
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Differential Expression Analysis between Clusters
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updated 2.7 years ago by • 0 • written 2.7 years ago by • 0
5
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5
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4.7k
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How to combine two DESeq2 objects (dds) for analysis
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updated 2.7 years ago by 43k • written 2.7 years ago by ▴ 10
1
vote
5
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2.9k
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How many parameters should be included in the model design for deseq2?
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2.7 years ago • updated 2.6 years ago Weiqian ▴ 10
2
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2
replies
931
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How Can I Assess the Reliability of BCV (Square-Root Dispersion) in Non-Replicated Experiments for Differential Expression Analysis Using edgeR?
edgeR
2.7 years ago f_rahmdani • 0
1
vote
2
replies
1.5k
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Removing Unwanted Variations
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2.7 years ago AZ ▴ 30
1
vote
3
replies
1.3k
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Recount3 data correspond to TCGA data
recount3
updated 10 months ago by ★ 1.1k • written 2.7 years ago by • 0
0
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1
reply
2.4k
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biomaRt - NameSpace loading failed
biomaRt bioma
updated 2.7 years ago by ★ 6.6k • written 2.7 years ago by • 0
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2
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GSVA with and without absolute scaling method
GSVA
2.7 years ago arashdeep singh • 0
0
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1
reply
971
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Plotting read densities from DiffBind results
Read density DiffBind
updated 2.7 years ago by ★ 5.2k • written 2.7 years ago by ▴ 20
0
votes
2
replies
1.2k
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Question regarding multiple comparisons in DiffBind
DiffBind
2.7 years ago • updated 2.6 years ago epipally • 0
2
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8
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4.4k
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Error in DGEList(counts = cnt, group = group) : non-numeric values found in counts
edgeR
2.7 years ago • updated 2.5 years ago Luis • 0
0
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2
replies
1.6k
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ModuleExprScore function/ hdWGNCA
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2.7 years ago Yuko • 0
0
votes
0
replies
864
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News: Bioconductor Release 3.16 Code Freeze
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2.7 years ago shepherl 4.2k
0
votes
1
reply
1.1k
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Mapping of probe IDs to gene gene symbols for Affymetrix Human Clariom D Assay platform
GeneMapping AnnotationDbi AffymetrixDataTestFiles GeneExpressionSignature org.Hs.eg.db
updated 2.7 years ago by 68k • written 2.7 years ago by • 0
4
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2
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3.8k
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Normalisation of data using DESeq2 with multi-groups
DEseq2
2.7 years ago Changsuk ▴ 10
0
votes
2
replies
824
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DESeq2 design matrix accounting for high heterogeneity of individuals inside a group
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2.7 years ago a.wag • 0
2
votes
2
replies
1.2k
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Question about transforming log expression values to antilog values in limma
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2.7 years ago Abdul ▴ 20
1
vote
1
reply
920
views
Can I run deseq2 on two separate experiments at once?
rnaseq deseq2
updated 2.7 years ago by ★ 5.0k • written 2.7 years ago by • 0
46,691 results • Page 55 of 934
Recent ...
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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…
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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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