Showing : RNA-SEQ • reset
2
votes
3
replies
191
views
TPM from STAR mapped counts
GeneExpression GenomicFeatures RNA-Seq TPM
updated 3 days ago by 48k • written 7 days ago by • 0
0
votes
3
replies
227
views
RNAseq (Deseq2 and Dexseq2) analysis on two time points with expected same effect
DEXSeq RNA-seq DESeq2
updated 21 days ago by ★ 1.9k • written 21 days ago by • 0
3
votes
4
replies
342
views
lfcShrink() and batch effects in DESeq2
BatchEffect lfcshrink RNA-seq DESeq2
6 weeks ago Eva ▴ 10
0
votes
3
replies
365
views
Fishpond with unbalanced dataset
rna-seq salmon fishpond swish
updated 3 months ago by 40k • written 3 months ago by • 0
5
votes
7
replies
563
views
Question about setting threshold using filtering by expression on genes in edgeR
filtering RNA-Seq CPM edgeR filterByExpr
updated 3 months ago by 48k • written 3 months ago by ▴ 10
0
votes
3
replies
381
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 4 months ago by 63k • written 4 months ago by • 0
0
votes
3
replies
414
views
Why is RNA-Seq library size not constant among samples?
RNA-Seq sequencer library_size sequency_depth multiplexing offtopic
updated 4 months ago by 63k • written 4 months ago by • 0
1
vote
1
reply
483
views
FPKM t-test vs DEseq2
DESeq2 statistics rna-seq
updated 5 months ago by ★ 3.4k • written 5 months ago by • 0
0
votes
1
reply
272
views
Access modalities in h5 files to extract expression and atac data from 10xh5
rna-seq Read10X_h5 atac modalities
updated 5 months ago by 63k • written 5 months ago by • 0
2
votes
2
replies
376
views
Multifactorial Design for DESEQ2
DESeq2 rna-seq
updated 5 months ago by ★ 3.4k • written 6 months ago by • 0
0
votes
1
reply
305
views
Job: Reopened: 'Omics data analyst for HPCBio, University of Illinois
SingleCell Spatial RNA-seq
7 months ago Jenny Drnevich ★ 2.0k
0
votes
1
reply
420
views
Error in DESeqDataSetFromHTSeqCount
DESeq2 RNA-seq HTseq DESeqDataSetFromHTSeqCount
updated 9 months ago by 40k • written 10 months ago by • 0
5
votes
9
replies
1.2k
views
GSVA perfomed on RSEM Expected Count data
GSVA RNA-Seq RSEM Expected_Count
14 months ago Yang Shi ▴ 10
2
votes
2
replies
745
views
How to judge DEG analysis of these samples could be done by using limma::voom
limma Clustering voom RNA-Seq
14 months ago Yang Shi ▴ 10
0
votes
0
replies
584
views
Job: Computational Biology Contractor - Chinook Therapeutics
Patient_stratification Multi-omics RNA-seq Kidney_Disease
14 months ago eolson • 0
2
votes
2
replies
616
views
How to deal with stronger effect by donor than treatment
MDS RNA-Seq
updated 14 months ago by 48k • written 14 months ago by • 0
0
votes
2
replies
1.4k
views
Incorporating spike-ins to rna-seq analysis
Spike-in RNASeqR DESeq2 Normalization rna-seq
updated 22 days ago by • 0 • written 17 months ago by • 0
5
votes
5
replies
1.2k
views
First principal component variance stabilised RNA-seq data correlates with total read counts per sample / library concentration
RNA-seq PCA control DESeq2 Quality
19 months ago • updated 16 months ago 9906201a ▴ 20
1
vote
5
replies
1.3k
views
featureCounts parameter queries - minOverlap, fracOverlap, fracOverlapFeature
subread Rsubread featureCounts RNA-seq
19 months ago Lucy ▴ 60
1
vote
3
replies
953
views
Two Genotypes Four Treatments RNA-seq Analysis
salmon rna-seq swish bootstrap fishpond
updated 19 months ago by 40k • written 19 months ago by • 0
0
votes
1
reply
682
views
First time Statistical Analysis of RNA-seq
edgeR RNA-Seq log2 foldchange q_value
updated 20 months ago by 48k • written 20 months ago by • 0
0
votes
5
replies
862
views
DTU analysis with tximport-DRIM-Seq-DEXSeq-stageR workflow starting from StrinTie output
RNA-seq DRIMSeq DEXSeq rnaseqDTU
2.1 years ago bioinformatic_trainee ▴ 10
0
votes
0
replies
628
views
Job: Senior Bioinformatician - University of Alabama at Birmingham
JobPosting Transcriptomics SingleCell RNA-seq
2.2 years ago lianov • 0
0
votes
1
reply
668
views
Interaction using a single factor model DESeq2
synergy DESeq2 RNA-seq contrast
2.2 years ago • updated 2.1 years ago slcno • 0
3
votes
5
replies
1.9k
views
Negative binomial fitting DESeq2
DESeq2 RNA-seq
updated 2.3 years ago by 40k • written 2.3 years ago by ▴ 60
0
votes
1
reply
968
views
Doing differential expression using FPKM , samples don't have replication
dge fpkm rna-seq
updated 2.3 years ago by 3.8k • written 2.3 years ago by • 0
2
votes
3
replies
908
views
Differential expression error in edgeR - maybe from design matrix?
design edgeR matrix RNA-seq MDplot
updated 2.3 years ago by 48k • written 2.3 years ago by • 0
1
vote
1
reply
1.3k
views
Correlation analyses on TCGA data
RNA-seq Normalization edgeR recount3
updated 2.3 years ago by ★ 1.0k • written 2.3 years ago by ▴ 20
3
votes
4
replies
784
views
need help regarding differential expression analysis
rna-seq
updated 2.3 years ago by 3.8k • written 2.3 years ago by ▴ 20
0
votes
0
replies
682
views
Job: Computational Biologist, Blood Research Institute, Versiti, Wauwatosa, Wisconsin, USA
RNA-seq Job Single-Cell
2.3 years ago rbrns • 0
3
votes
4
replies
1.1k
views
Pipeline for an Anova-like analysis in edgeR
edgeR anova rna-seq
2.4 years ago Antonio M. • 0
1
vote
2
replies
809
views
multifactorial design matrix
designmatrix RNA-seq limma
updated 2.5 years ago by 48k • written 2.5 years ago by ▴ 20
0
votes
5
replies
2.5k
views
How to remove batch effect from RNA-seq without count data?
RUVSeq FPKM removeBatchEffect RNA-seq sva
updated 20 months ago by ★ 3.4k • written 2.5 years ago by • 0
1
vote
7
replies
1.1k
views
how to make a contrast of uniquely DE genes
edgeR limma RNA-seq DEGseq
2.5 years ago decppced • 0
1
vote
3
replies
646
views
Questions regarding DESeq2 experimental setup and lfcShrink
DESeq2 RNA-seq
updated 2.5 years ago by 40k • written 2.5 years ago by • 0
0
votes
0
replies
689
views
Normalization for WGCNA on two organisms (virus-host)
RNA-Seq DESeq2 WGCNA Normalization
2.7 years ago wrzl • 0
0
votes
1
reply
738
views
Limma/Voom Normalized Counts
limma RNA-seq
updated 2.8 years ago by 48k • written 2.8 years ago by • 0
3
votes
9
replies
1.7k
views
summarizeToGene from tximeta: not all 'rnames' found or unique.
RNA-seq tximeta
2.8 years ago Pufall, Miles A ▴ 30
0
votes
2
replies
1.0k
views
RNA-seq read simulation for benchmarking differential expression/splicing variance
polyester simulation RNA-seq syntheticdata
updated 2.8 years ago by 48k • written 2.8 years ago by ▴ 70
0
votes
2
replies
883
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 4 months ago by • 0 • written 2.9 years ago by • 0
3
votes
6
replies
2.3k
views
DESeq2: When to split multiple group samples for 'more' accurate sizefactors, dispersions etc.
Dispersion RNA-seq DESeq2 Multiple-group
updated 2.6 years ago by 40k • written 2.9 years ago by ▴ 10
0
votes
3
replies
850
views
Weird set of samples in plant gene atlas study that appear over-corrected after DESeq2 normalization
RNA-Seq DESeq2
updated 2.9 years ago by 40k • written 2.9 years ago by • 0
0
votes
0
replies
1.1k
views
how to find consensus modules between 2 datasets by different platform through WGCNA
consensusmodule microarray RNA-seq WGCNA
2.9 years ago modarzi ▴ 10
0
votes
0
replies
691
views
Job: Bioinformatics Developer / Computational Biologist
bioinformatics rna-seq shiny apps R algorithm development Job
2.9 years ago mmartin ▴ 20
0
votes
3
replies
1.0k
views
GSVA on gene sets with 2 genes
GSVA gene sets RNA-seq
updated 2.9 years ago by ★ 3.0k • written 2.9 years ago by ▴ 70
0
votes
0
replies
621
views
circRNAprofiler - miRNA binding sites
circRNA RNA-seq circRNAprofiler
2.9 years ago Terra • 0
0
votes
0
replies
1.0k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
3.0 years ago ra711 • 0
3
votes
3
replies
880
views
Problem to understand Interactions at any time
RNA-seq edgeR interactions
updated 3.0 years ago by 48k • written 3.0 years ago by ▴ 10
0
votes
3
replies
960
views
Pathway analysis of bacterial RNA-seq data
annotation rna-seq pathway analysis
3.0 years ago microPhD • 0
3
votes
1
reply
689
views
How do you create a targets dataframe in edgeR?
edgeR RNA-SEQ
updated 3.0 years ago by 63k • written 3.0 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: Speeding up of DelayedArray::write_block() by Hervé Pagès 16k
Hi Koki, sorry for not seeing this before. > will SparseArraySeed in DelayedArray be replaced by this new sparse array format? Yes it wil…
Comment: Manual creation of qPCRset does not work by Ed Siefker ▴ 230
Thanks! This works for me.
Answer: Manual creation of qPCRset does not work by James W. MacDonald 63k
``` > mat <- matrix(rnorm(6*96), ncol = 6, nrow = 96, byrow = FALSE) > pd <- new("AnnotatedDataFrame", data = data.frame(1:6, row.names …
Answer: ukb Chromosomal position information was converted into SNPS by James W. MacDonald 63k
In my work, we almost always convert RSIDs to chr:pos because the former is ambiguous and changing whereas the latter is not. Which is like…
Comment: T.fit function of maSigPro returns error message by hanna.g • 0
Addition to the issue above: the T.fit function works only when choosing the step.method = "forward", for whatever reason. Maybe this clue …
Votes
Answer: Manual creation of qPCRset does not work
Answer: MDS plot edgeR
A: legend with gradient in ComplexHeatmap
Comment: comparing contrasts in edger/lima using makeContrasts function
Answer: comparing contrasts in edger/lima using makeContrasts function
Awards • All
Popular Question to komal.rathi ▴ 110
Popular Question to Levi Waldron 1.1k
Popular Question to Lucas Schiffer ▴ 240
Popular Question to Ed Siefker ▴ 230
Popular Question to James W. MacDonald 63k
Locations • All
United States, 11 minutes ago
Seattle, WA, United States, 12 minutes ago
United States, 13 minutes ago
Germany, 20 minutes ago
WEHI, Melbourne, Australia, 45 minutes ago
Traffic: 1050 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6