Showing : RNA-SEQ • reset
5
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2
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24k
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DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
written 5.7 years ago by ▴ 30
2
votes
5
replies
690
views
Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 12 weeks ago by ★ 4.4k • written 4 months ago by • 0
1
vote
3
replies
437
views
Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 3 months ago by 67k • written 3 months ago by ▴ 50
0
votes
1
reply
859
views
How to arrange multiple plots into one page in NOISeq?
noiseq RNA-seq quality control
updated 3 months ago by • 0 • written 5.1 years ago by ▴ 80
2
votes
4
replies
553
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 3 months ago by 42k • written 4 months ago by • 0
1
vote
2
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505
views
Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
4 months ago Dylan.Sheerin • 0
3
votes
3
replies
633
views
permutation test in edgeR
rna-seq edgeR
updated 4 months ago by 51k • written 5 months ago by • 0
9
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12
replies
8.3k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 5 months ago by • 0 • written 9.2 years ago by ▴ 30
0
votes
1
reply
1.1k
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 9 months ago by ★ 4.4k • written 6.4 years ago by • 0
0
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2
replies
467
views
WGCNA less samples
RNA-Seq WGCNA Worms
9 months ago davca • 0
0
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4
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994
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
11 months ago ar14g12 • 0
0
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2
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3.9k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 4.2 years ago by ▴ 80
2
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3
replies
2.7k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 12 months ago by 51k • written 12 months ago by • 0
0
votes
3
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890
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 12 months ago by ★ 1.9k • written 12 months ago by • 0
0
votes
2
replies
2.8k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 12 months ago by • 0 • written 2.4 years ago by • 0
3
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4
replies
1.1k
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
13 months ago Eva ▴ 10
0
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10
replies
2.5k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR rna-seq splice-variants
written 5.5 years ago by • 0
0
votes
3
replies
839
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 15 months ago by 42k • written 15 months ago by • 0
5
votes
7
replies
1.5k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 15 months ago by 51k • written 15 months ago by ▴ 10
0
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2
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1.4k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 16 months ago by • 0 • written 3.9 years ago by • 0
0
votes
3
replies
1.0k
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 16 months ago by 67k • written 16 months ago by • 0
0
votes
3
replies
905
views
Is the gene-specific PCR efficiency a serious concern for intrasample comparisons in RNA-Seq?
RNA-Seq normalization PCR_efficiency bias intrasample_comparison
updated 16 months ago by 67k • written 16 months ago by • 0
1
vote
1
reply
1.9k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 17 months ago by ★ 4.4k • written 17 months ago by • 0
0
votes
1
reply
873
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 17 months ago by 67k • written 17 months ago by • 0
2
votes
2
replies
934
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 18 months ago by ★ 4.4k • written 18 months ago by • 0
0
votes
1
reply
797
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
19 months ago Jenny Drnevich ★ 2.0k
1
vote
4
replies
1.2k
views
Nested paired design with covariates in limma
RNA-seq Nested paired design limma
updated 19 months ago by 51k • written 4.5 years ago by • 0
4
votes
8
replies
2.5k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 19 months ago by 67k • written 4.3 years ago by ▴ 30
0
votes
1
reply
908
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 21 months ago by 42k • written 22 months ago by • 0
6
votes
6
replies
6.6k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 23 months ago by ▴ 200 • written 6.3 years ago by ▴ 10
5
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9
replies
2.2k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.1 years ago Yang Shi ▴ 10
2
votes
2
replies
1.4k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
2.2 years ago • updated 2.1 years ago Yang Shi ▴ 10
0
votes
0
replies
1.0k
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
2.2 years ago eolson • 0
2
votes
2
replies
1.1k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 2.2 years ago by 51k • written 2.2 years ago by • 0
3
votes
2
replies
5.9k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 2.3 years ago by ▴ 10 • written 4.1 years ago by ▴ 80
5
votes
5
replies
1.9k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.6 years ago • updated 2.4 years ago 9906201a ▴ 20
3
votes
3
replies
3.7k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.5 years ago by ▴ 30 • written 5.6 years ago by ▴ 40
0
votes
2
replies
3.9k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 2.5 years ago by • 0 • written 6.6 years ago by • 0
1
vote
5
replies
2.4k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.6 years ago Lucy ▴ 60
1
vote
3
replies
1.6k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.6 years ago by 42k • written 2.6 years ago by • 0
0
votes
5
replies
4.2k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.7 years ago by ★ 4.4k • written 3.5 years ago by • 0
0
votes
1
reply
1.0k
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.7 years ago by 51k • written 2.7 years ago by • 0
0
votes
7
replies
2.6k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 2.9 years ago by • 0 • written 7.3 years ago by ▴ 40
5
votes
12
replies
5.9k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 2.9 years ago by ▴ 30 • written 7.0 years ago by ▴ 40
1
vote
1
reply
3.1k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 3.1 years ago by ▴ 10 • written 4.2 years ago by ▴ 10
0
votes
1
reply
1.1k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.2 years ago • updated 3.1 years ago slcno • 0
0
votes
1
reply
1.7k
views
igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 3.1 years ago by 51k • written 5.5 years ago by • 0
0
votes
5
replies
1.4k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
3.1 years ago bioinformatic_trainee ▴ 10
0
votes
0
replies
1.0k
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.1 years ago lianov • 0
3
votes
5
replies
3.0k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 3.3 years ago by 42k • written 3.3 years ago by ▴ 60
50 results • Page 1 of 1
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Comment: How to read OSCA book? by zr • 0
Got it, that had really confused me a bit, thank you for your help!
Comment: How to use removeBatchEffect for removing effect of multiple confounding variabl by James W. MacDonald 67k
Please don't add questions onto a four-year old post. Instead, start a new one. If you want to reference the old post, that's fine.
Answer: How to use removeBatchEffect for removing effect of multiple confounding variabl by bioinformata • 0
Is it feasible to remove batch effect with limma after variance stabilizing transformation of the gene expression , or is eough to use vst…
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by James W. MacDonald 67k
Hi Guido, It's that last filtering step. You are saying the NCBI Gene ID has to be unique AND the ontology has to be BP, which isn't what …
Comment: AffylmGUI does not start wit R 4.4.1 by richardallenfriedmanbrooklyn ▴ 20
Gordon, I found out what went wrong. The problem was that the xquartz distribution for mac from cran did not include tcltk! I found that b…
Votes
Answer: How to read OSCA book?
Answer: How to read OSCA book?
DESeq2 design and contrasts with 2 drug-treated and one control group
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
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