Showing : RNAseq • reset
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sva and svaseq for unsupervised analysis of expression data
sva combat gene expression batch effect rnaseq
updated 10.1 years ago by ▴ 650 • written 10.1 years ago by ▴ 10
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1
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1.4k
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Is it possible (or does it make sense) to display two different gene sets in one PCA-plot?
pca deseq2 rnaseq
updated 10.1 years ago by 43k • written 10.1 years ago by ▴ 270
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2
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1.8k
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Considering both : batch effect and patient to patient variation in EdgeR analysis
EdgeR batch effect patient rnaseq
10.1 years ago n.deshpande • 0
1
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8
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2.7k
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EdgeR GLM using blocking analysis
EdgeR rnaseq
updated 10.1 years ago by ★ 29k • written 10.1 years ago by ▴ 90
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2
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1.7k
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Using merged alignments of PE readlists for DEXSeq
dexseq paired rnaseq samtools merge
updated 10.1 years ago by ★ 1.9k • written 10.1 years ago by • 0
1
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3
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2.7k
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summarizeOverlaps bplapply error
genomicalignments genomicranges bioconductor rnaseq
updated 10.2 years ago by • 0 • written 10.7 years ago by • 0
5
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6
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4.2k
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Principal component plot of the RNAseq samples and DEseq2 result
deseq2 rnaseq
updated 10.2 years ago by 43k • written 10.2 years ago by ▴ 10
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2
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2.7k
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design matrix edge R pairwise comparison at different timepoints after infection with replicates
RNASeq edgeR RNASeq edgeR
updated 10.2 years ago by • 0 • written 13.3 years ago by ▴ 70
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0
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1.7k
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Error: non-character argument in DEXSeqDataSetFromHTSeq from DEXSeq
dexseq rnaseq differential exon usage
10.2 years ago arom2 • 0
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2
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1.2k
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plotMDS: metric or non-metric method?
edger rnaseq
10.2 years ago martha.nigg.1 • 0
2
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1
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4.8k
views
DESeq 2 two factor design
deseq2 R rnaseq
updated 10.2 years ago by 43k • written 10.2 years ago by • 0
3
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13
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5.4k
views
RPKM and FPKM
rnaseq
10.2 years ago Asma rabe ▴ 290
2
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1
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4.0k
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RNA-seq Differential expression using 3 groups
rnaseq anova deseq2 edger genespring
10.2 years ago BM • 0
0
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2
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1.9k
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An error in RNA-Seq workflow at the gene level
rnaseq
updated 10.2 years ago by 25k • written 10.2 years ago by • 0
4
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14
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10k
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Extracting custom post-normalization counts from DESeq2
deseq2 r ruvseq normalization rnaseq
10.3 years ago • updated 10.2 years ago nickp60 • 0
1
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2
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2.1k
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Error message running DE-test in Monocle
monocle cummerbund DE rnaseq
updated 10.3 years ago by • 0 • written 10.5 years ago by ▴ 270
4
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4
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2.1k
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Does the BAM need to be sorted by name for "summarizeOverlaps" of "GenomicAlignments"
genomicalignments deseq2 rnaseq
updated 10.3 years ago by ★ 6.8k • written 10.3 years ago by ▴ 230
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0
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1.2k
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Matching New Samples to Differential Expression Profile
differential expression ebseq rnaseq
10.3 years ago jbarker2 • 0
11
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0
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6.5k
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Tutorial: Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges Annotation RNAseq visualization Tutorial
10.3 years ago Martin Morgan 25k
0
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1
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2.5k
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trying to use ballgown with Sailfish/Salmon pipeline
rnaseq multi-mapped reads ballgown salmon timecourse
10.3 years ago friederike.mgh • 0
2
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6
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2.7k
views
derfinder gets stuck in calculatePvalues
derfinder software error rnaseq
10.3 years ago drramki.chop • 0
0
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0
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1.7k
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How to fully use the list of DEGs in non model species?
deseq2 gage ebseq rnaseq
10.3 years ago jackipchiho ▴ 10
0
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1
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1.6k
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How to interpret the fusion.txt file output from subjunc (Rsubread package)
rsubread subjunc rnaseq fusion genes
updated 10.3 years ago by ★ 3.6k • written 10.3 years ago by • 0
1
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3
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1.8k
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GenomicFeatures error: rsqlite_query_send: could not execute1: database or disk is full
genomicfeatures rnaseq deseq2
10.3 years ago Xiaokuan Wei ▴ 230
1
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4
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1.5k
views
how to get the differentially expressed genes that only affected by one factor within multiple factors
deseq2 rnaseq
updated 10.3 years ago by 43k • written 10.3 years ago by • 0
17
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4
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33k
views
RPKM, CPM and TMM
edger rnaseq differential expression
updated 10.3 years ago by ★ 29k • written 10.3 years ago by ▴ 160
6
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1
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4.5k
views
Tutorial: Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
rnaseq biocparallel workflows sra Tutorial
10.3 years ago Sean Davis 21k
8
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0
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4.1k
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Tutorial: Statistics and Computing in Genome Science (CSAMA) Course Material
rnaseq chipseq visualization metagenomics proteomics Tutorial
10.3 years ago Martin Morgan 25k
5
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4
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2.1k
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Multiple Testing Correction
limma rnaseq moderated t-test
10.3 years ago ea1402 ▴ 20
2
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4
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4.1k
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report genes in intersection of Venn diagram with topTable?
rnaseq venn diagram limma toptable edgeR
updated 10.3 years ago by 53k • written 10.3 years ago by • 0
7
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6
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2.3k
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edgeR (3.10.2) contrast question for experimental factors combined as a group
edgeR rnaseq multiple factor design
updated 10.3 years ago by ★ 7.9k • written 10.3 years ago by • 0
1
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3
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2.5k
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Visualizing gene counts and variance stabilization
deseq2 rnaseq variancestabilizingtransformation visualization
updated 10.3 years ago by 43k • written 10.3 years ago by ▴ 40
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1
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1.4k
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gene expression analysis using fuzzy C-means by using Mfuzz package
rnaseq
updated 10.3 years ago by ▴ 370 • written 10.3 years ago by • 0
2
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5
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4.2k
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How to use q.value cutt off in "decideTests" function for RNAseq differential expression analysis
rnaseq decideTests limma qvalue
10.3 years ago anver • 0
0
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3
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1.9k
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PCA analysis of the RNASeq data
rnaseq R
10.3 years ago Emily • 0
1
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1
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1.6k
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EdgeR--multi-factorial nested design
edger nested design rnaseq
updated 10.4 years ago by ★ 7.9k • written 10.4 years ago by • 0
3
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6
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3.4k
views
RNAseq multifactor experiment limma design with patient and batch effects
limma rnaseq batcheffect
updated 10.4 years ago by • 0 • written 10.9 years ago by ▴ 10
1
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1
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2.6k
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Display error (error bars) for fold-change estimate from replicates in edgeR
edger rnaseq
updated 10.4 years ago by ★ 29k • written 10.4 years ago by • 0
0
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1
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3.6k
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Small-RNA analysis using DESeq2
rnaseq deseq2
updated 10.4 years ago by 43k • written 10.4 years ago by • 0
8
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11
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7.7k
views
[DESeq2] Cook's distance flagging for continuous variables
deseq2 rnaseq
updated 10.4 years ago by 43k • written 10.4 years ago by ▴ 680
0
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1
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1.2k
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missing values (NA) in spliceR results
splicer rnaseq
updated 10.4 years ago by ▴ 120 • written 11.0 years ago by ▴ 20
2
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7
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4.6k
views
mm10 ENSEMBL not available for GOSEQ
goseq RNAseq mm10
10.4 years ago Merienne Nicolas ▴ 120
5
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3
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3.0k
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edgeR: annotation and isoform analysis alternatives
edgeR ruvseq rnaseq isoforms
10.4 years ago sergio.espeso-gil • 0
0
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2
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2.9k
views
Error in CummeRbund installation
cummerbund rnaseq bioinformatics bioconductor R
updated 10.4 years ago by 68k • written 10.4 years ago by • 0
0
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0
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932
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RNAseq binary transformation
tcga binary rnaseq
10.4 years ago ezz • 0
8
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10
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27k
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Design formula and Design matrix in DESeq
rnaseq deseq2 formula Limma
10.4 years ago AurelieMLB ▴ 50
1
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4
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3.9k
views
Different clustering results of DESeq2 counts and rlog
tcga nomalization rnaseq deseq2
10.4 years ago ezz • 0
3
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5
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1.8k
views
weird model design for DE analysis
RNASeq
updated 11 weeks ago by 53k • written 12.2 years ago by ▴ 140
0
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1
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2.2k
views
Using PCA for unsupervised clustering of RNA-Seq with DESeq2
rnaseq pca deseq2 clustering
updated 10.4 years ago by 43k • written 10.4 years ago by ▴ 60
1
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3
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3.6k
views
DESeq2 effects of treatment at different time points including subject ID
deseq2 rnaseq differential gene expression
10.4 years ago Catalina Aguilar Hurtado ▴ 90
1,409 results • Page 23 of 29
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Answer: DESeq2 design for haplotype MPRA by Michael Love 43k
> My goal is to identify which non-reference haplotypes are differentially active compared to the corresponding ref/ref haplotype within ea…
Answer: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
It seems fine on devel as well. ``` > BSgenome.Hsapiens.UCSC.hg38 | BSgenome object for Human | - organism: Homo sapiens | - provide…
Comment: "organism" missing in BSgenome.Hsapiens.UCSC.hg38 slotNames by James W. MacDonald 68k
R-4.5.1 is compatible with both release and devel versions of Bioconductor. Which one are you using? I am still on release, and it's fine: …
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by umairmugal82 • 0
When accuracy matters in academic assessment, nothing should be left to chance. [Accurate grading made simple on EasyGrader.net][1] ensures…
Comment: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Votes
A: Different logFC (log2foldchange) values for genes from limma-voom and other too
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
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