Showing : RNA-seq • reset
2
votes
3
replies
179
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Too many significant genes when integrating gtex and tcga
RNA-seq DESeq2
updated 2 days ago by ★ 4.1k • written 3 days ago by • 0
3
votes
3
replies
339
views
permutation test in edgeR
rna-seq edgeR
updated 16 days ago by 50k • written 29 days ago by • 0
0
votes
1
reply
910
views
Human genes correlation to Bacterial genes
correlation pearsoncorrelation rna-seq differential gene expression
updated 4 months ago by ★ 4.1k • written 6.1 years ago by • 0
0
votes
2
replies
315
views
WGCNA less samples
RNA-Seq WGCNA Worms
5 months ago davca • 0
0
votes
4
replies
714
views
DESeq2 : standardising variation between treatments
RNA-seq DESeq2
7 months ago • updated 6 months ago ar14g12 • 0
0
votes
2
replies
3.5k
views
Dealing with multi-overlapping and multi-mapping reads
RNA-seq featureCounts ht-seq
written 3.8 years ago by ▴ 80
2
votes
3
replies
1.6k
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 7 months ago by 50k • written 7 months ago by • 0
0
votes
3
replies
661
views
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
3
votes
4
replies
877
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
9 months ago Eva ▴ 10
0
votes
3
replies
690
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 10 months ago by 42k • written 10 months ago by • 0
5
votes
7
replies
1.2k
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 11 months ago by 50k • written 11 months ago by ▴ 10
0
votes
3
replies
717
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 65k • written 12 months ago by • 0
0
votes
3
replies
860
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 65k • written 12 months ago by • 0
1
vote
1
reply
1.3k
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 12 months ago by ★ 4.1k • written 12 months ago by • 0
0
votes
1
reply
689
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 13 months ago by 65k • written 13 months ago by • 0
2
votes
2
replies
726
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 13 months ago by ★ 4.1k • written 13 months ago by • 0
0
votes
1
reply
667
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
15 months ago • updated 14 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
721
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 17 months ago by 42k • written 17 months ago by • 0
5
votes
9
replies
1.9k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
21 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
21 months ago Yang Shi ▴ 10
0
votes
0
replies
870
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
22 months ago eolson • 0
2
votes
2
replies
981
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
0
votes
2
replies
2.3k
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
votes
3
replies
3.3k
views
Using PEER to identify hidden confounders in RNA-seq data (not working)
PEER RNA-seq differential expression hidden confounders
updated 2.1 years ago by ▴ 30 • written 5.3 years ago by ▴ 30
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 2.0 years ago 9906201a ▴ 20
1
vote
5
replies
2.0k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
2.2 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 2.2 years ago by 42k • written 2.2 years ago by • 0
0
votes
5
replies
3.6k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 2.3 years ago by ★ 4.1k • written 3.1 years ago by • 0
0
votes
1
reply
900
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 2.3 years ago by 50k • written 2.3 years ago by • 0
1
vote
1
reply
2.6k
views
create S-plots with ropls package
s-plot ropls opls-da rna-seq
updated 2.7 years ago by ▴ 10 • written 3.9 years ago by ▴ 10
0
votes
5
replies
1.2k
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.7 years ago bioinformatic_trainee ▴ 10
0
votes
0
replies
913
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.8 years ago lianov • 0
0
votes
1
reply
1.0k
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.8 years ago • updated 2.7 years ago slcno • 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
0
votes
1
reply
1.6k
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 2.9 years ago by ★ 3.9k • written 2.9 years ago by • 0
2
votes
3
replies
1.2k
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 2.9 years ago by 50k • written 2.9 years ago by • 0
5
votes
2
replies
21k
views
DESeq2: thousands of NA for pvalues?
deseq2 rna-seq DEGs cooks cutoff
updated 2.3 years ago by • 0 • written 5.3 years ago by ▴ 30
1
vote
1
reply
1.7k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 2.9 years ago by ★ 1.0k • written 3.0 years ago by ▴ 20
3
votes
4
replies
1.1k
views
need help regarding differential expression analysis
rna-seq
updated 3.0 years ago by ★ 3.9k • written 3.0 years ago by ▴ 20
0
votes
0
replies
948
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
3.0 years ago rbrns • 0
1
vote
4
replies
3.8k
views
NA values of count matrix in class DESeqDataSet
rna-seq recount
updated 3.0 years ago by ★ 1.0k • written 6.6 years ago by • 0
3
votes
4
replies
1.4k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
3.0 years ago Antonio M. • 0
1
vote
2
replies
1.1k
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 3.1 years ago by 50k • written 3.1 years ago by ▴ 20
1
vote
7
replies
1.4k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
3.1 years ago decppced • 0
1
vote
3
replies
850
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 3.2 years ago by 42k • written 3.2 years ago by • 0
0
votes
0
replies
876
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
3.3 years ago wrzl • 0
3
votes
9
replies
2.2k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
3.4 years ago Pufall, Miles A ▴ 30
0
votes
1
reply
1.0k
views
Limma/Voom Normalized Counts
limma RNA-seq
updated 3.4 years ago by 50k • written 3.4 years ago by • 0
0
votes
2
replies
1.5k
views
RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 3.5 years ago by 50k • written 3.5 years ago by ▴ 70
0
votes
2
replies
1.2k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 12 months ago by • 0 • written 3.5 years ago by • 0
50 results • Page 1 of 1
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Answer: Recovering my account credentials on Bioconductor by shepherl 3.9k
As we will need to exchange some information can you please contact me at bioconductorcoreteam@gmail.com and I can better assist you. Che…
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Votes
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
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