Showing : rnaseq • reset
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sva and svaseq for unsupervised analysis of expression data
sva combat gene expression batch effect rnaseq
updated 10.2 years ago by ▴ 650 • written 10.2 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 10.2 years ago by 43k • written 10.2 years ago by ▴ 270
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2
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1.9k
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Considering both : batch effect and patient to patient variation in EdgeR analysis
EdgeR batch effect patient rnaseq
10.2 years ago n.deshpande • 0
1
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8
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2.8k
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EdgeR GLM using blocking analysis
EdgeR rnaseq
updated 10.2 years ago by ★ 29k • written 10.2 years ago by ▴ 90
0
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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 10.2 years ago by ★ 1.9k • written 10.2 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 10.3 years ago by • 0 • written 10.8 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 10.3 years ago by 43k • written 10.3 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 10.3 years ago by • 0 • written 13.4 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
10.3 years ago arom2 • 0
1
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2
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1.2k
views
plotMDS: metric or non-metric method?
edger rnaseq
10.3 years ago martha.nigg.1 • 0
2
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1
reply
4.8k
views
DESeq 2 two factor design
deseq2 R rnaseq
updated 10.3 years ago by 43k • written 10.3 years ago by • 0
3
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13
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5.4k
views
RPKM and FPKM
rnaseq
10.3 years ago Asma rabe ▴ 290
2
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1
reply
4.0k
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RNA-seq Differential expression using 3 groups
rnaseq anova deseq2 edger genespring
10.3 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 10.3 years ago by 25k • written 10.3 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
10.4 years ago • updated 10.3 years ago nickp60 • 0
1
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2
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2.2k
views
Error message running DE-test in Monocle
monocle cummerbund DE rnaseq
updated 10.4 years ago by • 0 • written 10.6 years ago by ▴ 270
4
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4
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2.2k
views
Does the BAM need to be sorted by name for "summarizeOverlaps" of "GenomicAlignments"
genomicalignments deseq2 rnaseq
updated 10.4 years ago by ★ 6.8k • written 10.4 years ago by ▴ 230
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0
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1.2k
views
Matching New Samples to Differential Expression Profile
differential expression ebseq rnaseq
10.4 years ago jbarker2 • 0
11
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0
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6.5k
views
Tutorial: Introduction to Bioconductor for high-throughput sequence analysis
GenomicRanges Annotation RNAseq visualization Tutorial
10.4 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
10.4 years ago friederike.mgh • 0
2
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6
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2.8k
views
derfinder gets stuck in calculatePvalues
derfinder software error rnaseq
10.4 years ago drramki.chop • 0
0
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0
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1.7k
views
How to fully use the list of DEGs in non model species?
deseq2 gage ebseq rnaseq
10.4 years ago jackipchiho ▴ 10
0
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1
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1.7k
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How to interpret the fusion.txt file output from subjunc (Rsubread package)
rsubread subjunc rnaseq fusion genes
updated 10.4 years ago by ★ 3.6k • written 10.4 years ago by • 0
1
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3
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1.8k
views
GenomicFeatures error: rsqlite_query_send: could not execute1: database or disk is full
genomicfeatures rnaseq deseq2
10.4 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 10.4 years ago by 43k • written 10.4 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 10.4 years ago by ★ 29k • written 10.4 years ago by ▴ 160
6
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1
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4.6k
views
Tutorial: Orchestrating a small, parallel, RNA-seq pre-processing workflow using R
rnaseq biocparallel workflows sra Tutorial
10.4 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
10.4 years ago Martin Morgan 25k
5
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4
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2.2k
views
Multiple Testing Correction
limma rnaseq moderated t-test
10.4 years ago ea1402 ▴ 20
2
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4
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4.2k
views
report genes in intersection of Venn diagram with topTable?
rnaseq venn diagram limma toptable edgeR
updated 10.4 years ago by 53k • written 10.4 years ago by • 0
7
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6
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2.4k
views
edgeR (3.10.2) contrast question for experimental factors combined as a group
edgeR rnaseq multiple factor design
updated 10.4 years ago by ★ 7.9k • written 10.4 years ago by • 0
1
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3
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2.5k
views
Visualizing gene counts and variance stabilization
deseq2 rnaseq variancestabilizingtransformation visualization
updated 10.4 years ago by 43k • written 10.4 years ago by ▴ 40
0
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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 10.4 years ago by ▴ 370 • written 10.4 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
10.4 years ago anver • 0
0
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3
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1.9k
views
PCA analysis of the RNASeq data
rnaseq R
10.4 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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3.5k
views
RNAseq multifactor experiment limma design with patient and batch effects
limma rnaseq batcheffect
updated 10.5 years ago by • 0 • written 11.0 years ago by ▴ 10
1
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1
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2.7k
views
Display error (error bars) for fold-change estimate from replicates in edgeR
edger rnaseq
updated 10.5 years ago by ★ 29k • written 10.5 years ago by • 0
0
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1
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3.6k
views
Small-RNA analysis using DESeq2
rnaseq deseq2
updated 10.5 years ago by 43k • written 10.5 years ago by • 0
8
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11
replies
7.7k
views
[DESeq2] Cook's distance flagging for continuous variables
deseq2 rnaseq
updated 10.5 years ago by 43k • written 10.5 years ago by ▴ 680
0
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1
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1.3k
views
missing values (NA) in spliceR results
splicer rnaseq
updated 10.5 years ago by ▴ 120 • written 11.1 years ago by ▴ 20
2
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7
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4.7k
views
mm10 ENSEMBL not available for GOSEQ
goseq RNAseq mm10
10.5 years ago Merienne Nicolas ▴ 120
5
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3
replies
3.1k
views
edgeR: annotation and isoform analysis alternatives
edgeR ruvseq rnaseq isoforms
10.5 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 10.5 years ago by 68k • written 10.5 years ago by • 0
0
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0
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944
views
RNAseq binary transformation
tcga binary rnaseq
10.5 years ago ezz • 0
8
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10
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27k
views
Design formula and Design matrix in DESeq
rnaseq deseq2 formula Limma
10.5 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
10.5 years ago ezz • 0
3
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5
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1.9k
views
weird model design for DE analysis
RNASeq
updated 3 months ago by 53k • written 12.3 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 10.5 years ago by 43k • written 10.5 years ago by ▴ 60
1
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3
replies
3.6k
views
DESeq2 effects of treatment at different time points including subject ID
deseq2 rnaseq differential gene expression
10.5 years ago Catalina Aguilar Hurtado ▴ 90
1,409 results • Page 23 of 29
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Comment: Alternative to BrainArray custom CDF packages for Affymetrix chips? by insuraasanaa3scetaxrealty • 0
Lamento que el acceso a los paquetes BrainArray esté fallando; cuando ocurren estos problemas, es util contar con recursos alternativos bie…
Comment: Getting a large intercept with DESeq2 by Denise • 0
Hi, Thank you very much, James and Michael, for getting back to me! I noticed the large intercept when plotting the coefficients returned …
Comment: Error installing Seqinfo by shepherl 4.2k
Yes and we are working on getting the updated windows binaries distributed asap! We are hopeful by the end of this week
Comment: APAlyzer by shepherl 4.2k
We apologize for their unresponsiveness; you could try posting your question here to see if anyone in the community could assist in the me…
Answer: Error installing Seqinfo by fabio.marroni • 0
I am answering my own question. I found the solution thanks to [this post][1], and I am writing here the very simple procedure: 1) Instal…
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Answer: replace cat with message in glmTreat when lfc = 0
Answer: replace cat with message in glmTreat when lfc = 0
Comment: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
Answer: Issues with downloading biomaRt - SeqInfo and S4 Vectors
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