Showing : RnaSeq • reset
1
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Trying to simplify Interaction analysis with edger, and propably failing to do so?
rnaseq edger interactions multiple factor design differential gene expression
7.6 years ago David R ▴ 90
0
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0
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1.4k
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Job: Postdoctoral Position: Posttranscriptional gene regulation in T cells (analysis of RNAseq, metabolomics)
Basel switzerland RNAseq metabolomics Job
7.6 years ago Robert Ivanek ▴ 750
0
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4
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5.9k
views
Change point size and remove outline in scater's plotPCA
scater rnaseq single-cell
updated 7.6 years ago by • 0 • written 8.5 years ago by ▴ 70
3
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2
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2.0k
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Repeated Measures, Within-Subject, Between-Groups RNAseq Analysis
edgeR rnaseq repeated measures
updated 7.6 years ago by ★ 7.9k • written 7.6 years ago by • 0
0
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1
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2.0k
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Error while Installing DESeq2
software error R deseq2 rnaseq
updated 7.6 years ago by 43k • written 7.6 years ago by • 0
2
votes
18
replies
4.3k
views
Using tximport on rsem files produces error while trying to read in files
R tximport rnaseq tpm rsem
7.7 years ago • updated 7.6 years ago stephan.emmrich ▴ 10
0
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1
reply
693
views
Time-series Experiments with Varied Drug Concentrations Design Matri
deseq2 rnaseq
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
1
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1
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1.4k
views
DESeq2 confounding cartridge
deseq2 confounders nanostring rnaseq differential gene expression
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
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2
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3.9k
views
Going crazy with normalizing TCGA raw rsem gene count
cancer tcga normalization rnaseq differential gene expression
updated 7.7 years ago by • 0 • written 10.6 years ago by • 0
1
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1
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1.3k
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How to compare RNA-seq counts matrices from different aligners ?
rnaseq counts alignement
7.7 years ago Aurora ▴ 20
7
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8
replies
15k
views
DESeq2: one condition vs multiple combined
rnaseq deseq2
updated 7.7 years ago by ▴ 10 • written 9.3 years ago by ▴ 40
1
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0
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2.8k
views
topGO (Version: 2.30.1) - weight01 algorithm
topgo gene ontology pathway analysis rnaseq DEG
7.7 years ago digrigor ▴ 10
0
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28
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4.6k
views
Job: Postdoc on integrating and analyzing new transcriptome types in the Bgee database
rnaseq data integration single-cell pacbio across species Job
7.7 years ago bgee • 0
0
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1
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1.3k
views
GenomicFeatures: could not find symbol "recursive" in environment of the generic function
genomicfeatures rnaseq txdb
7.7 years ago lucasmacielbiotec • 0
1
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4
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3.2k
views
If transcript-to-gene conversion is needed in kallisto > tximport > DESeq2 pipeline
deseq2 rnaseq kallisto tximport
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
7
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10
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7.6k
views
Justification for collapsing technical replicates in DESeq2
deseq2 rnaseq replicate differential expression
updated 7.7 years ago by ▴ 30 • written 9.3 years ago by ▴ 50
0
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5
replies
1.4k
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DESeq2: normalization of experiments sequenced separately
RNAseq normalization deseq2
7.7 years ago uguy • 0
0
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0
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1.4k
views
Job: Biostatistician III @ Duke University
rnaseq precision medicine biomarker genomics Job
7.7 years ago ram330 • 0
1
vote
1
reply
873
views
edgeR: Subset DGEList by treatment-specific expression
rnaseq edger
updated 7.7 years ago by ★ 29k • written 7.7 years ago by • 0
7
votes
11
replies
3.4k
views
Analysis of pathways using edgeR
rnaseq differential expression edgeR kegg
updated 7.7 years ago by 53k • written 7.7 years ago by ▴ 60
2
votes
2
replies
1.8k
views
ASpli ERROR during the counting step
ASpli rnaseq
updated 7.7 years ago by ▴ 10 • written 8.0 years ago by ▴ 10
1
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2
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3.3k
views
use tximport's countsFromAbundance when using DESeq2
deseq2 tximport normalization salmon rnaseq
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
1
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3
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1.5k
views
plotMA (DESeq2) Issue
deseq2 plotMA rnaseq logfoldchange
updated 7.7 years ago by 43k • written 7.7 years ago by • 0
0
votes
0
replies
623
views
summarizeOverlaps to count stranded single-end RNA-seq dara
rnaseq
7.7 years ago yinyuan • 0
1
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4
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2.0k
views
problem of getting count matrix in featurecounts of Rsubread package
rnaseq rsubread featurecounts
updated 7.7 years ago by ★ 3.6k • written 7.8 years ago by • 0
2
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2
replies
1.5k
views
tximport failing at importing TPM instead of FPKM
tximport rnaseq rsem
updated 7.7 years ago by • 0 • written 7.7 years ago by • 0
5
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4
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2.1k
views
Glimma Interactive plots for RNAseq
Glimma R markdown rnaseq
7.7 years ago Aurora ▴ 20
2
votes
2
replies
996
views
Normalize for changes in one direction
limma voom rnaseq
updated 7.8 years ago by ★ 29k • written 7.8 years ago by ▴ 90
2
votes
1
reply
1.1k
views
DESeq2-No replicates-Utility of log2fold shrunk values?
deseq2 rnaseq
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
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8
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6.6k
views
Comparing between two differential expression analysis - two different fold changes
Deseq deseq2 differential gene expression rnaseq statistical test
7.8 years ago Marina ▴ 40
0
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2
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4.5k
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DESeq2 followed by goseq GO-analysis: Extracting DE genes of enriched GO category
deseq2 goseq rnaseq go enrichment differential gene expression
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
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4
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1.8k
views
Normalise counts when tumour samples have normal tissue contamination.
deseq2 deseq edgeR rnaseq htseqcounts
7.8 years ago Deepali • 0
0
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0
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1.7k
views
Job: Senior Bioinformatician, Children's Cancer Research Institute Vienna, Austria
postdoc rnaseq NGS WGS bioinformatician job Job
7.8 years ago da.de ▴ 30
0
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1
reply
1.9k
views
MA plot interpretation .
MAPLOT DESEQ2 RNASEQ
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
5
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9
replies
4.3k
views
Correct version of EnsDb.Hsapiens for ensembl transcriptome
ensembldb ensembl release rnaseq salmon tximport
7.8 years ago emmak ▴ 20
3
votes
4
replies
2.7k
views
edgeR - comparing treatment groups across multiple populations
rnaseq edger
updated 7.8 years ago by ★ 29k • written 7.8 years ago by • 0
1
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3
replies
1.0k
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rna-seq analysis with limma shows only 1 differential expressed gene
limma rnaseq
updated 7.8 years ago by • 0 • written 7.8 years ago by • 0
4
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7
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3.7k
views
DESeq2 vs TCGAbiolinks normalization methods
normalization rnaseq deseq2
updated 4.0 years ago by • 0 • written 7.8 years ago by ▴ 420
1
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1
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2.4k
views
How can I retrieve the gene names of my count matrix?
rnaseq summarizeoverlaps count matrix
updated 7.8 years ago by 68k • written 7.8 years ago by • 0
3
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4
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3.4k
views
DESeq2 batch effect modeling and matrix not full rank
deseq2 rnaseq rna-seq
updated 7.8 years ago by 43k • written 7.8 years ago by ▴ 20
2
votes
2
replies
1.1k
views
Moderated F-statistics for time course experiment
limma rnaseq
updated 7.8 years ago by 53k • written 7.8 years ago by ▴ 130
0
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0
replies
1.1k
views
Subset functionin R
R ballgown rnaseq
7.8 years ago amy16 • 0
0
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4
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1.3k
views
can DESeq2 be used to compare these miRNA read counts from 9 samples?
deseq2 rnaseq
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
0
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0
replies
1.1k
views
Accessing the assembly data-output
R rnaseq ballgown
7.8 years ago amy16 • 0
1
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1
reply
1.4k
views
Expression deconvolution using PSEA: applicable to RNA-seq?
deconvolution rnaseq psea
7.8 years ago WouterDeCoster ▴ 130
1
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1
reply
2.6k
views
WGCNA - Choosing the best threshold
wgcna sft picksoftthreshold threshold rnaseq
updated 7.8 years ago by ★ 3.0k • written 7.8 years ago by ▴ 40
4
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5
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3.1k
views
MasigPro and estimation of theta for negative binomial law
R masigpro edgr rnaseq negative binomial model
7.8 years ago nicolas.hipp ▴ 20
0
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3
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1.5k
views
upperquartile with voom
limma-voom rnaseq normalization
7.8 years ago bilcodygm • 0
0
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2
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1.6k
views
assess quality of data
rnaseq edger limma-voom
updated 7.8 years ago by 43k • written 7.8 years ago by • 0
2
votes
2
replies
2.3k
views
RNAseq analysis: how to compare two very different samples?
edgeR deseq2 RNAseq
updated 7.8 years ago by ★ 29k • written 7.9 years ago by ▴ 10
1,410 results • Page 14 of 29
Recent ...
Replies
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0
Thank you very much, @ATpoint and @kevin , for your valuable insights. I have carefully checked all your suggestions. First, I examined th…
Answer: Finding duplicated entries in GRangesList by Kevin Blighe ★ 4.0k
The duplicated and unique functions operate element-wise on GRangesList objects. This means that they apply the respective function to each…
Answer: DESeq2 on non-RNASeq counts data by Kevin Blighe ★ 4.0k
The use of DESeq2 for count data from artificial sequences is acceptable, as the program models counts via a negative binomial distribution…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hello Rui Tang, The buffer overflow error in featureCounts that you encountered is likely due to a compatibility issue between the Subre…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
The issue that you describe with the tumor mutational burden (TMB) plots appearing linear and lacking consistent TMB values across samples …
Votes
Answer: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Post translational modifications and phosphoproteomics in limpa?
Answer: Identifying differentially expressed genes in individual samples from a large co
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