Showing : RNA-SEQ • reset
1
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Including infectivity information to RNA-Seq analysis
RNASeqData DESeq2 RNA-Seq RNASeq
updated 3 months ago by 67k • written 3 months ago by ▴ 50
2
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4
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564
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DESeq2- Mysterious interaction suppresses DEGs
DESeq2 PCAplot RNA-Seq DesignModel
updated 4 months ago by 42k • written 4 months ago by • 0
1
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2
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510
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Multi-factorial, longitudinal disease progression analysis with unbalanced patient sampling - duplicateCorrelation or blocking?
rna-seq duplicateCorrelation limma voom
4 months ago Dylan.Sheerin • 0
2
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5
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698
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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
3
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3
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649
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permutation test in edgeR
rna-seq edgeR
updated 5 months ago by 51k • written 5 months ago by • 0
0
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2
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467
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WGCNA less samples
RNA-Seq WGCNA Worms
10 months ago davca • 0
0
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4
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997
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DESeq2 : standardising variation between treatments
RNA-seq DESeq2
11 months ago ar14g12 • 0
2
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3
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2.7k
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TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 12 months ago by 51k • written 12 months ago by • 0
0
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3
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895
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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
3
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4
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1.1k
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lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
13 months ago Eva ▴ 10
0
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3
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843
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Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 15 months ago by 42k • written 15 months ago by • 0
5
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7
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1.5k
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Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 16 months ago by 51k • written 16 months ago by ▴ 10
0
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3
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910
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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
0
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3
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1.0k
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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
1
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1
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1.9k
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FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 17 months ago by ★ 4.4k • written 17 months ago by • 0
0
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1
reply
879
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 18 months ago by 67k • written 18 months ago by • 0
2
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2
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941
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Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 18 months ago by ★ 4.4k • written 18 months ago by • 0
0
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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
0
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1
reply
912
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Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 22 months ago by 42k • written 22 months ago by • 0
5
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9
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2.2k
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GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
2.2 years ago • updated 2.1 years ago Yang Shi ▴ 10
2
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2
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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 Yang Shi ▴ 10
0
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0
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1.0k
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Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
2.2 years ago eolson • 0
2
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2
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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
0
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2
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2.9k
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
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
1
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5
replies
2.4k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.6 years ago Lucy ▴ 60
1
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3
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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
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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
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5
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1.5k
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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
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0
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1.0k
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Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
3.2 years ago lianov • 0
0
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1
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1.1k
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Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
3.2 years ago • updated 3.1 years ago slcno • 0
3
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5
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3.0k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 3.3 years ago by 42k • written 3.3 years ago by ▴ 60
0
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1
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2.0k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 3.3 years ago by ★ 4.0k • written 3.3 years ago by • 0
2
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3
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1.4k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 3.3 years ago by 51k • written 3.3 years ago by • 0
1
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1
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1.8k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 3.3 years ago by ★ 1.1k • written 3.3 years ago by ▴ 20
3
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4
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1.2k
views
need help regarding differential expression analysis
rna-seq
updated 3.3 years ago by ★ 4.0k • written 3.3 years ago by ▴ 20
0
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0
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1.1k
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.3 years ago rbrns • 0
3
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4
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1.6k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.4 years ago Antonio M. • 0
1
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2
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1.2k
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multifactorial design matrix
designmatrix RNA-seq limma
updated 3.5 years ago by 51k • written 3.5 years ago by ▴ 20
0
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5
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4.3k
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
1
vote
7
replies
1.6k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.5 years ago decppced • 0
1
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3
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950
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 3.5 years ago by 42k • written 3.5 years ago by • 0
0
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0
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996
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
3.6 years ago wrzl • 0
0
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1
reply
1.2k
views
Limma/Voom Normalized Counts
limma RNA-seq
updated 3.8 years ago by 51k • written 3.8 years ago by • 0
3
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9
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2.5k
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summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
3.8 years ago Pufall, Miles A ▴ 30
0
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2
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1.8k
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RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 3.8 years ago by 51k • written 3.8 years ago by ▴ 70
0
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2
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1.4k
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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
3
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6
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3.3k
views
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion RNA-seq DESeq2 Multiple-group
updated 3.6 years ago by 42k • written 3.9 years ago by ▴ 10
0
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3
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1.3k
views
Weird set of samples in plant gene atlas study that appear over-corrected after DESeq2 normalization
RNA-Seq DESeq2
updated 3.9 years ago by 42k • written 3.9 years ago by • 0
0
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0
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1.4k
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how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule microarray RNA-seq WGCNA
3.9 years ago modarzi ▴ 10
50 results • Page 1 of 1
Recent ...
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Answer: rtracklayer accessing UCSC data table not working by James W. MacDonald 67k
The track argument is deprecated now, so you can omit it. ``` > tbl.rmsk <- getTable(ucscTableQuery(mySession, table = "rmsk", range = …
Answer: For feline genome by James W. MacDonald 67k
This support site is meant to help people with specific questions about using Bioconductor software. There is a [vignette for `ROntoTools`]…
Comment: DESeq2 with proteomics data by Michael Love 42k
I would guess the distribution isn't correct. Anyway I agree it's not a good idea to supply non-sequencing data to a method designed for se…
Answer: Many DEGs (Is a high percentage of DEGs acceptable in DESeq2)? by Michael Love 42k
Let me copy over my answers from GitHub 1. this is not a violation of the size factor calculation. check `plotPCA`, likely the groups a…
Answer: Rstudio died when put more than three letters in subseting a SummarizedExperime by Shuo GG • 0
The problem is solved. It's because Rstudio try to autocomplete or suggest objects from the environment, even though I don't understand why…
Votes
Comment: Error in GOmeth function of missMethyl when EPICv2 annotation is used
Answer: unable to access Annotationhub latest record
How to keep cells square in heatplot function of enrichplot
Answer: Inconsistent result in edgeR
A: MBDseq analysis using qsea package
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