4
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2
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1.1k
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A way to find which genome builds a package supports
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2.7 years ago Dmitry • 0
1
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1
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1.3k
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Error when running getGDCprojects()
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2.7 years ago DevelopingHippo • 0
0
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3
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ChAMP filter bug when using beta matrix and pd as input
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2
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2
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Question about avereps function of limma
avereps probes average limma Microarray
updated 2.8 years ago by 53k • written 2.8 years ago by ▴ 10
1
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4
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Single-cell differential expression analysis with multiple samples
SingleCell
2.8 years ago iaradsouza1 • 0
3
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6
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1.8k
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News: Bioconductor will rename the default branch on `git.bioconductor.org` to `devel`
Software Bioconductor Devel devel
updated 2.7 years ago by • 0 • written 2.8 years ago by 4.2k
0
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8
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2.0k
views
fail to annotate chromosome data to single cell object
error SingleCell annotate
updated 2.1 years ago by • 0 • written 2.8 years ago by • 0
1
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9
replies
3.9k
views
conumee with Infinium MethylationEPIC v2.0
MethylationEPICv2.0 conumee
updated 12 months ago by • 0 • written 2.8 years ago by ▴ 50
3
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4
replies
1.9k
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Error with importFrom and GenomicRanges in NAMESPACE
GenomicRanges IRanges
updated 2.7 years ago by 16k • written 2.8 years ago by • 0
4
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5
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2.9k
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Pseudo-bulk celltype comparison across conditions from multiple-sources
DESeq2 edgeR scRNAseq
updated 2.8 years ago by ▴ 760 • written 2.8 years ago by ▴ 10
0
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0
replies
726
views
Can I use default parameter settings of DiffBind to analyze m6A-seq data?
DiffBind MeRIP-seq m6A-seq
2.8 years ago zhiyi • 0
0
votes
1
reply
1.2k
views
Heatmap of two conditions from the normalized gene count data
GeneExpression heatmaps
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
0
votes
1
reply
1.1k
views
Normalization of RNA seq data before DESeq2 and PCA in case of strong batch effects
DESeq2 Normalization sva
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
2
votes
3
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1.6k
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BigWig files provided by recount3
recount3
updated 2.8 years ago by ★ 1.1k • written 2.8 years ago by ▴ 20
0
votes
1
reply
1.4k
views
Analyse of MASS spectrometry proteomics data
DifferentialExpression MassSpectrometry
updated 2.8 years ago by • 0 • written 3.3 years ago by • 0
0
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2
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4.0k
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biomaRt to match UniProt protein IDs with protein names
Proteomics UniProtKeywords
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
1
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2
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1.9k
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how i can get the name of genes in pathway?
chipseq ChIPseeker
2.8 years ago chavaleab • 0
1
vote
3
replies
997
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DESeq2 check failure on Linux ARM64
DESeq2
updated 2.8 years ago by 43k • written 2.8 years ago by ▴ 10
2
votes
6
replies
1.8k
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No enriched GO terms CpGs
DNAMethylation missMethyl
updated 2.8 years ago by ▴ 40 • written 2.8 years ago by • 0
0
votes
1
reply
953
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Filter the GRN networks based on the optimal scale-free topology (SFT)
GRN BioNERO
updated 2.8 years ago by ▴ 40 • written 2.8 years ago by • 0
2
votes
1
reply
1.5k
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How to identify the batch informations from the sample ID?
TCGAbiolinks BatchQC BatchEffect
updated 2.3 years ago by • 0 • written 2.8 years ago by ▴ 200
0
votes
0
replies
535
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DMRcaller Neighborhood method
DMRcaller
2.8 years ago Sarah • 0
5
votes
2
replies
2.5k
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Support for new Illumina human methylation EPIC array v2
human methylationArrayAnalysis
updated 4 months ago by • 0 • written 2.8 years ago by ▴ 80
0
votes
4
replies
2.0k
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Sex estimation problems in [estimateCellCounts]: methylation arrays
methylationArrayAnalysis minfiData minfi MethylationArrayData MethylationArray
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
0
votes
1
reply
831
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Definition of disease_subtype abbreviations
curatedMetagenomicData
updated 2.7 years ago by ▴ 240 • written 2.8 years ago by ▴ 10
0
votes
4
replies
1.9k
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how to extract list in quantile in R
R quantile list
2.8 years ago sat • 0
3
votes
10
replies
5.4k
views
Is there any chance to solve "the model matrix is not full rank" in DESeq2?
DESeq2
2.8 years ago Sep • 0
0
votes
0
replies
1.3k
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Job: Open position in the CBIO lab: single-cell proteomics
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2.8 years ago Laurent Gatto 1.6k
2
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2
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2.5k
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STRINGdb offline use (via input_directory argument)
STRINGdb
2.8 years ago Charlotte Soneson ▴ 170
3
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2
replies
1.5k
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Batch question Bulk RNA-Seq
BatchEffect RNASeq
2.8 years ago chf • 0
0
votes
0
replies
1.3k
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KM Plot for gene of interest (e.g. TP53) using TCGA-PAAD dataset
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2.8 years ago Manav • 0
2
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9
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3.4k
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featureCounts with NCBI T2T not capturing all genes
CHM13v2.0 featureCounts T2T Rsubread
2.8 years ago Hilary ▴ 40
0
votes
2
replies
1.7k
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Could not find function "Standard Chromosomes"
scrna scRNAseq
updated 2.1 years ago by • 0 • written 2.8 years ago by • 0
0
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2
replies
1.2k
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Is there any reason to think that normalization (e.g. TMM) doesn't work well with samples that that have very different raw counts?
limma RNASeqData edgeR
updated 2.8 years ago by ▴ 40 • written 2.8 years ago by • 0
0
votes
1
reply
1.4k
views
Which samples to remove from analysis based on Cook's distance outliers plot
DESeq2 cooks outliers
updated 2.8 years ago by ★ 5.0k • written 2.8 years ago by • 0
1
vote
1
reply
1.5k
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champ.load IDAT files from subdirectories
ChAMP
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
0
votes
0
replies
1.0k
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Can ChiPseeker be as highly customizable as "computeMatrix"? for example if I want to plot the distribution of genes on the TAD boundary?
deeptools ChIPseeker
2.8 years ago 840842906 • 0
0
votes
3
replies
1.3k
views
MaSigPro Single Series Analysis
maSigPro
updated 2.8 years ago by • 0 • written 5.8 years ago by • 0
0
votes
0
replies
575
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Single Series Time Course
tissueTreg
2.8 years ago guang-hui • 0
0
votes
0
replies
863
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data truncation with sce2fcs()
CATALYST
2.8 years ago Shaun • 0
0
votes
1
reply
960
views
analysis of DE and TF by CeTF
RIF PCIT CeTF
updated 2.8 years ago by • 0 • written 2.8 years ago by • 0
1
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3
replies
1.7k
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Analysing Genome Studio .txt files with minfi
minfi
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
0
votes
5
replies
2.3k
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minfi error read.metharray.exp
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written 2.8 years ago by • 0
0
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3
replies
1.1k
views
Battery gene sets for CAMERA limma
CAMERA
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
0
votes
3
replies
1.1k
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Error with makeOrgPackageFromNCBI - no information found for species with tax id
makeOrgPackageFromNCBI
updated 2.8 years ago by 68k • written 2.8 years ago by • 0
1
vote
8
replies
2.4k
views
Understandig listValues argument of DESEQ in multiple group comparisons
DESeq2
updated 2.7 years ago by 43k • written 3.8 years ago by • 0
1
vote
7
replies
2.7k
views
Likelihood ratio test (lrTest) in MAST comparing full to reduced model; and another question on controlling for CDR
MAST
2.8 years ago • updated 2.7 years ago Ken C • 0
0
votes
1
reply
1.0k
views
BioC packages in cancer genomics
genomics cancer
updated 2.8 years ago by ★ 4.0k • written 2.8 years ago by ▴ 670
0
votes
0
replies
464
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How to draw the MEM matrix of cell annotation
MatrixDiagram
2.8 years ago shuangshuang • 0
0
votes
1
reply
943
views
Microarray Data - Matching Probe ID's to Gene Expression Symbols
limma
updated 2.8 years ago by ★ 4.0k • written 2.8 years ago by • 0
46,691 results • Page 59 of 934
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Replies
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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