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More Web Proxy on the site http://driver.im/
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fail to use addPerROIQC in Rmd
stand standR
updated 29 days ago by • 0 • written 29 days ago by • 0
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399
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how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
minfi DMRcate
29 days ago • updated 12 days ago xiaofeiwang198266 • 0
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Crossover design with limma
limma crossover
updated 15 days ago by 52k • written 4 weeks ago by ▴ 30
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9
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851
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Differential Expression Genes as Independent Variables
limma DifferentialExpression variancePartition dream
updated 27 days ago by 67k • written 4 weeks ago by • 0
6
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10
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What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 23 days ago by ★ 4.6k • written 4 weeks ago by ▴ 10
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reply
181
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rrvgo::calculateSimMatrix() error
rrvgo
updated 4 weeks ago by • 0 • written 4 weeks ago by • 0
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123
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Job: 3x PhD positions in UK: cool algorithms and impactful applications
JobPosting
4 weeks ago Daphne • 0
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248
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DESeq2 sizefactors counfounded with biological treatment
DESeq2
5 weeks ago • updated 4 weeks ago Anna • 0
2
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1
reply
260
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bioconductor packages on bioconda
Bioconductor
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
1
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4
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323
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txdb.mmusculus.ucsc.mm10.knowngene issue on X chromosome
TxDb.Mmusculus.UCSC.mm10.ensGene TxDb karyoploteR
5 weeks ago remi-xavier.coux ▴ 10
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312
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Epic v2 Annotation CpG_maf source?
MethylationArray methy EPICv2manifest
5 weeks ago Meghan • 0
1
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3
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417
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Struggle with the replicates of epic array data
limma epicarray IlluminaHumanMethylationEPICanno.ilm10b2.hg19
written 5 weeks ago by • 0
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125
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Lipidomics Barplot: raw values or non-log, lipidr-normalized values?
Normalization Lipidomics lipidr
5 weeks ago David R ▴ 90
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Spam: <img/src/
genomes rgu34cprobe
5 weeks ago <img/src/ 0
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531
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Deseq2 res Function
DESeq2
updated 5 weeks ago by 67k • written 5 weeks ago by ▴ 10
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880
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ANOVA like approach of edgeR
edgeR
updated 4 weeks ago by 52k • written 5 weeks ago by ▴ 10
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422
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Create Illmina bead summary data
beadarray Illuminabeadchip GenomeStudio lumi
5 weeks ago Liu • 0
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4
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406
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Help with RSEM counts: do I transpose matrix?
RSEM DESeq2
5 weeks ago NB • 0
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1
reply
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Detecting genomic signatures of drug resistance breast cancer in transcriptomic data
TransOmicsData signatureSearchData StatisticalMethod
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
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1
reply
166
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WGCNA with TPM tables
RNASeq WGCNA ComparativeGenomics
updated 5 weeks ago by ★ 4.6k • written 5 weeks ago by • 0
2
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5
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806
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Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ("trying to load regions beyond the boundaries of non-circular sequenc…
genomes BSgenome.Mmusculus.UCSC.mm39
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
0
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5
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403
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Identical samples after deseq2 batch effect removal
DESeq2
updated 5 weeks ago by 43k • written 5 weeks ago by • 0
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1
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229
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DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 different genotypes
DESeq2
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
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1
reply
504
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BiocNeighbours Utility for k-Nearest Neighbour Classification
Classification BiocNeighbors
updated 5 weeks ago by 67k • written 6 weeks ago by ★ 1.5k
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1
reply
163
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HilBertVis install error
HilbertVis ChIPseqR
updated 5 weeks ago by 67k • written 5 weeks ago by • 0
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2
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258
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Downloading Metagenomic Data with Higher Taxonomic Units
curatedMetagenomicData
updated 5 weeks ago by ★ 1.1k • written 10 weeks ago by • 0
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111
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Job: Post-Doctoral Research Fellow - Cancer Immunotherapy
JobPosting
5 weeks ago Fred Hutch (Recruiting) ▴ 40
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339
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Spam: Unlocking Potential: NURS FPX Strategies and Insights
levi NURSFPX ragene20sttranscriptcluster.db ssrch
written 8 months ago by 0
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295
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Differene between the Wald and LRT test for time-series gene expression data
DESeq2
5 weeks ago Denise • 0
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554
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Is it recommended to analyze different tissues together when using edgeR
DifferentialExpression edgeR
updated 5 weeks ago by 52k • written 6 weeks ago by • 0
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439
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Handling Epic Array Data
minfi
6 weeks ago • updated 5 weeks ago Melisa Tecik • 0
1
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423
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Allele frequencies for ALL alleles of one SNP ?
Bioconductor
6 weeks ago • updated 5 weeks ago Abiologist • 0
2
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330
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preprocessIllumina error with EPICv2 array
minfi EPICv2manifest
6 weeks ago Rakesh • 0
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195
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List of DEGs belonging to an Agilent-single color microarray experiment using Limma package
limma
6 weeks ago giulia.gentile ▴ 10
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308
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CleanUpRNAseq with a GTF that is missing mitochondria annotation data
CleanUpRNAseq
6 weeks ago • updated 5 weeks ago rcreed • 0
1
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1
reply
151
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UniProt.ws query loading indefinitely
UniProt.ws
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
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392
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Identifying potentially associated gene set to drug response using GSVA
drug RNASeq GSVA
updated 20 hours ago by • 0 • written 6 weeks ago by • 0
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285
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How to get The evolutionary conservation scores for lncRNAs by the phastCons100way.UCSC.hg38 (3.7.1) R package
txdbmaker GenomicScores phastCons100way.UCSC.hg38 GenomicFeatures
6 weeks ago rania.alanany • 0
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Are unequal sample sizes in differential gene expression (DGE) analysis a problem for edgeR, DESeq2, and NOISeq? Could you give me some advice on how…
RNA RNASeqPower DEGseq
updated 6 weeks ago by 52k • written 6 weeks ago by • 0
4
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2
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546
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Using voom-transformed counts for unsupervised analyses (PCA, Random Forest, Elastic Net): Best practices?
limma limma-voom
updated 6 weeks ago by 52k • written 6 weeks ago by ▴ 50
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Package needs internet access
BSgenome BSgenome.Hsapiens.UCSC.hg38 Offline
updated 6 weeks ago by 67k • written 6 weeks ago by ▴ 20
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2
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186
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Limma Interaction Effect with Covariates
limma DMRcate
6 weeks ago kitzhu • 0
2
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1
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204
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Using Affymetrix Custom Array
ArrayExpress makecdfenv AffymetrixChip gcrma GeneExpression
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
1
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2
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257
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Harmonizing Gene Annotations for Meta-Analysis of GSE68183 and GSE80178
GEOquery
updated 6 weeks ago by 67k • written 6 weeks ago by • 0
0
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1
reply
151
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eRNAs count
RNASeq DESeq2
updated 6 weeks ago by ★ 4.6k • written 6 weeks ago by • 0
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0
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131
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Job: Postdoctoral position in Computational Epigenomics of Aging and Cancer
Aging Epigenetics JobPosting Postdoctor Cancer
6 weeks ago xiaolong • 0
0
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1
reply
394
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DESeq2 rerun returns different results
DESeq2
updated 6 weeks ago by ★ 4.6k • written 6 weeks ago by • 0
2
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3
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891
views
[How to construct a model.matrix ]
limma modelmatrix
updated 6 weeks ago by 52k • written 6 weeks ago by • 0
0
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1
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233
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Is my time course analysis with DESeq2 valid?
GeneExpression DESeq2 TimeCourse
updated 6 weeks ago by 43k • written 7 weeks ago by • 0
6
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6
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4.0k
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WGCNA coupled with differential expression analysis: question about baseline module detection
wgcna WGCNA
written 4.7 years ago by ▴ 60
46,256 results • Page 2 of 926
Recent ...
Replies
Comment: Identifying potentially associated gene set to drug response using GSVA by coolmathforkids2 • 0
It is always helpful to see clear explanations and solutions for bioconductor related challenges. Posts like this make the community a valu…
Comment: minfi latest update for EPIC V2 chip by macdonaldfrench7286566 • 0
Yes, the most updated analysis for the EPIC V2 chip using the minfi package still involves using the annotations provided by jokergoo. *Th…
Answer: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k
To compute CPM values from edgeR: ``` y <- DGEList(counts = counts, samples = samples, genes = genes, group = samples$Disease_status) y <- …
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k
Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.
Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0
But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…
Votes
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor
A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
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