Showing : RNA-seq • reset
0
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735
views
How to arrange multiple plots into one page in NOISeq?
noiseq RNA-seq quality control
updated 4 days ago by • 0 • written 4.8 years ago by ▴ 80
2
votes
4
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228
views
DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 5 days ago by 42k • written 8 days ago by • 0
1
vote
2
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306
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
17 days ago • updated 16 days ago Dylan.Sheerin • 0
2
votes
3
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276
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 20 days ago by ★ 4.2k • written 22 days ago by • 0
3
votes
3
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377
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permutation test in edgeR
rna-seq edgeR
updated 5 weeks ago by 50k • written 6 weeks ago by • 0
9
votes
12
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7.9k
views
Multi factor design edgeR/Deseq2
deseq2 edgeR rna-seq
updated 5 weeks ago by • 0 • written 8.9 years ago by ▴ 30
0
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1
reply
926
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 5 months ago by ★ 4.2k • written 6.1 years ago by • 0
0
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2
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334
views
WGCNA less samples
RNA-Seq WGCNA Worms
6 months ago davca • 0
0
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4
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737
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
7 months ago ar14g12 • 0
0
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2
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3.6k
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Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.8 years ago by ▴ 80
2
votes
3
replies
1.8k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 8 months ago by 50k • written 8 months ago by • 0
0
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3
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704
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RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 8 months ago by ★ 1.9k • written 8 months ago by • 0
0
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2
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2.4k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 8 months ago by • 0 • written 2.1 years ago by • 0
3
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4
replies
903
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
0
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10
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2.3k
views
Error in reading data on isoformswitchanalyzeR
isoformswitchanalyzeR rna-seq splice-variants
written 5.1 years ago by • 0
0
votes
3
replies
719
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 11 months ago by 42k • written 11 months ago by • 0
5
votes
7
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1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 12 months ago by 50k • written 12 months ago by ▴ 10
0
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2
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1.3k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 12 months ago by • 0 • written 3.6 years ago by • 0
0
votes
3
replies
890
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 12 months ago by 66k • written 12 months ago by • 0
0
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3
replies
749
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 12 months ago by 66k • written 12 months ago by • 0
1
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1
reply
1.4k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 13 months ago by ★ 4.2k • written 13 months ago by • 0
0
votes
1
reply
717
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 14 months ago by 66k • written 14 months ago by • 0
2
votes
2
replies
754
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 14 months ago by ★ 4.2k • written 14 months ago by • 0
0
votes
1
reply
692
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
15 months ago Jenny Drnevich ★ 2.0k
1
vote
4
replies
1.0k
views
Nested paired design with covariates in limma
RNA-seq Nested paired design limma
updated 15 months ago by 50k • written 4.2 years ago by • 0
4
votes
8
replies
2.2k
views
Don't let TopGo to trimm long GO names
go software error topgo rna-seq
updated 15 months ago by 66k • written 4.0 years ago by ▴ 30
0
votes
1
reply
749
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 18 months ago by 42k • written 18 months ago by • 0
4
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6
replies
6.1k
views
strange results with featureCounts
RNA-seq featureCounts total RNA
updated 19 months ago by ▴ 20 • written 6.0 years ago by ▴ 10
5
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9
replies
1.9k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
22 months ago Yang Shi ▴ 10
2
votes
2
replies
1.2k
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
22 months ago Yang Shi ▴ 10
0
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0
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902
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
22 months ago eolson • 0
2
votes
2
replies
1.0k
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 22 months ago by 50k • written 22 months ago by • 0
3
votes
2
replies
5.2k
views
Calculation of module membership in WGCNA
WGCNA RNA-seq ModuleMembership Network Hub gene
updated 2.0 years ago by ▴ 10 • written 3.8 years ago by ▴ 80
5
votes
5
replies
1.6k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
2.2 years ago • updated 2.1 years ago 9906201a ▴ 20
3
votes
3
replies
3.4k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.2 years ago by ▴ 30 • written 5.3 years ago by ▴ 30
0
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2
replies
3.7k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 2.2 years ago by • 0 • written 6.3 years ago by • 0
1
vote
5
replies
2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.3 years ago Lucy ▴ 60
1
vote
3
replies
1.4k
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 2.3 years ago by 42k • written 2.3 years ago by • 0
5
votes
2
replies
22k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 2.3 years ago by • 0 • written 5.4 years ago by ▴ 30
0
votes
5
replies
3.7k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.4 years ago by ★ 4.2k • written 3.2 years ago by • 0
0
votes
1
reply
918
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.4 years ago by 50k • written 2.4 years ago by • 0
0
votes
7
replies
2.5k
views
Error reading kallisto files using tximport for cross species RNA-Seq analysis
kallisto tximport RNA-Seq across species
updated 2.6 years ago by • 0 • written 7.0 years ago by ▴ 40
5
votes
12
replies
5.6k
views
DESeq2 time series contrasts between timepoints
rna-seq deseq2
updated 2.6 years ago by ▴ 30 • written 6.7 years ago by ▴ 40
1
vote
1
reply
2.7k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 2.8 years ago by ▴ 10 • written 3.9 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.8 years ago slcno • 0
0
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1
reply
1.5k
views
igraph clustering for gene coexpression network
igraph network gene corexpression rna-seq
updated 2.8 years ago by 50k • written 5.2 years ago by • 0
0
votes
5
replies
1.3k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.8 years ago bioinformatic_trainee ▴ 10
0
votes
0
replies
935
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.8 years ago lianov • 0
3
votes
5
replies
2.6k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 2.9 years ago by 42k • written 2.9 years ago by ▴ 60
1
vote
1
reply
1.7k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.0 years ago by ★ 1.1k • written 3.0 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
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Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0
Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…
Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0
Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…
Comment: Cannot install oligo on Fedora by James W. MacDonald 66k
There is the `zlibbioc` package that provides the headers for zlib 1.2.5, that I think you should be able to use, although that would requi…
Answer: GSVA function by Robert Castelo ★ 3.3k
Hi, We recommend to input normalized expression values in logarithmic scale to GSVA. We also recommend to use the latest release of the …
Votes
DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol
DESeq2 swap ensembl gene id rownames with gene symbol column
A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge
DESeq2: add annotations (from data frame) to DESeqDataSet
Add new columns to DESeqResults from text file by matching rownames.
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