Showing : rnaseq • reset
0
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4
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261
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Using featureCounts with SAF annotation file gives "Error: only GTF files contain additional attributes"
RNASeq Rsubread
updated 3 days ago by ★ 3.6k • written 4 days ago by • 0
10
votes
11
replies
1.9k
views
SGSeq: moving toward diffex from SGSeq analysis
sgseq rnaseq
updated 5 days ago by • 0 • written 6.8 years ago by ▴ 80
2
votes
2
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150
views
Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data
NanoStringNCTools limma ExpressionData RNASeq edgeR
6 days ago mohammedtoufiq91 ▴ 10
1
vote
1
reply
203
views
How to remove batch effect to combine RNAseq data from 2 different experiments?
BatchQC BatchEffect RNASeq
updated 7 days ago by 66k • written 8 days ago by • 0
0
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0
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61
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scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
RNASeq scRNAseq
8 days ago Bibi • 0
1
vote
3
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291
views
How to approach time course RNAseq data? Seeing 80% DE genes in timepoint groups
DifferentialExpression TimeCourse timeOmics edgeR RNAseq
updated 13 days ago by 50k • written 14 days ago by • 0
5
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3
replies
333
views
Log-cpm values from limma
limma edgeR RNASeq
updated 18 days ago by 50k • written 5 weeks ago by • 0
0
votes
3
replies
249
views
Differences in differential analysis methods for RNA-Seq
DESeq2 StatisticalMethod Proteomics DifferentialExpression RNASeq
updated 25 days ago by ★ 4.2k • written 26 days ago by • 0
0
votes
2
replies
203
views
limma-voom: Calculate the log-fold change in gene expression within a sample
limma RNASeq voom
written 5 weeks ago by • 0
0
votes
1
reply
177
views
DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR)
DESeq2 RNAseq
updated 4 weeks ago by 42k • written 4 weeks ago by • 0
1
vote
3
replies
910
views
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
clusterProfiler RNASeq
updated 4 weeks ago by ★ 1.2k • written 15 months ago by ▴ 10
0
votes
2
replies
257
views
RNAseq:Technical replicates from different batches
technicalReplicates BatchEffect limma RNASeq
5 weeks ago catv • 0
0
votes
1
reply
141
views
ONT long-read RNA sequencing - data analysis options
DESeq2 LongRead DEXSeq IsoformSwitchAnalyzeR RNASeq
updated 5 weeks ago by 42k • written 5 weeks ago by • 0
0
votes
2
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975
views
Single-Cell Data Simulation from Bulk RNA-seq
SingleCell RNASeq RNASeqData scRNAseq
updated 5 weeks ago by • 0 • written 18 months ago by • 0
0
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1
reply
161
views
Can you find the correct transcript in scRNA seq data
scRNAseq RNAseq
updated 6 weeks ago by ★ 4.2k • written 7 weeks ago by • 0
0
votes
5
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1.8k
views
EdgeR: paired samples together with independant samples
RNASeq edgeR RNASeq edgeR
updated 8 weeks ago by 50k • written 11.6 years ago by ▴ 30
0
votes
2
replies
712
views
biomart not ound some prevous release
biomart rnaseq
written 5.3 years ago by ▴ 40
4
votes
16
replies
7.4k
views
Normalised counts from RUVg in RUVSeq
RUVg ruvseq rnaseq
updated 9 weeks ago by • 0 • written 9.0 years ago by ▴ 150
0
votes
2
replies
293
views
Filtering and Reference Level for DESeq2
DESeq2 GeneFiltering RNAseq
9 weeks ago kcarey • 0
0
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5
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9.4k
views
tximport all(file.exists(files)) is not TRUE
bioconductor tximport rnaseq R
updated 9 weeks ago by • 0 • written 7.7 years ago by • 0
0
votes
2
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340
views
RNA sequencing raw counts gene filtering
DESeq2 limma RNAseq
10 weeks ago kcarey • 0
2
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2
replies
295
views
Question about extracting co-efficients for pairwise comparisons in edgeR
limma fit design RNASeq edgeR
10 weeks ago Sabiha ▴ 20
0
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2
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1.3k
views
Should immunoglobulin genes be filtered out during RNA-seq differential expression analysis
RNASeq
updated 11 weeks ago by • 0 • written 2.8 years ago by • 0
1
vote
4
replies
344
views
DESeq2 Replicates
DESeq2 RNASeq
11 weeks ago kcarey • 0
1
vote
3
replies
400
views
DESEQ2 Batch Effect
DESeq2 BatchEffect RNASeq
updated 12 weeks ago by ★ 1.4k • written 12 weeks ago by ▴ 10
0
votes
3
replies
583
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 4 months ago by • 0
3
votes
5
replies
680
views
DESEQ Inquiry
DESeq2 rnaseqGene RNASeqData limma RNASeq
updated 12 weeks ago by 42k • written 3 months ago by ▴ 10
0
votes
4
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343
views
Interactions in batches of varying size with different number of replicates using limma
limma RNASeq DifferentialExpression
3 months ago • updated 12 weeks ago mperalc • 0
2
votes
5
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1.5k
views
edgeR Help: Getting no DGEs with an FDR < 0.05
edgeR RNASeq RNASeqData Bioconductor
written 15 months ago by • 0
0
votes
2
replies
365
views
Error in featureCounts matrix
GenomeWideAssociation countsimQC RNASeq
updated 3 months ago by 50k • written 3 months ago by • 0
2
votes
1
reply
282
views
Limma Question
DESeq2 BatchEffect limma RNASeq
updated 3 months ago by 42k • written 3 months ago by ▴ 10
3
votes
6
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617
views
Average biological replicates in RNA-seq
Mfuzz RNASeq
3 months ago boczniak767 ▴ 720
0
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0
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252
views
Differential expression analysis between different species
DEG RNASeqData DifferentialExpression SCBN RNASeq
3 months ago Abril • 0
4
votes
6
replies
662
views
filtering lowly expressed reads
RNASeq limma DifferentialExpression Preprocessing
updated 3 months ago by 50k • written 4 months ago by • 0
2
votes
2
replies
454
views
Graphing DEseq2 Normalized Counts using ggplot2
DESeq2 Normalization RNASeq
3 months ago jackafiore • 0
1
vote
2
replies
1.2k
views
How to combine a bulk and pseudobulk dataset?
DESeq2 limma RNASeq RNASeqData
written 12 months ago by • 0
0
votes
4
replies
451
views
Ballgown error in scan for c.tab files
ballgown RNASeq
3 months ago candacenewcome • 0
1
vote
3
replies
370
views
DESeq2 analysis on time-series RNA experiment
RNASeqData DESeq2 RNASeq
3 months ago island • 0
1
vote
3
replies
645
views
Comparing relative expression of a conserved gene between distantly related species.
ComparativeGenomics Normalization RNASeq DESeq2
written 4 months ago by • 0
0
votes
1
reply
269
views
Error in GDCRNATools
ceRNA GDCRNATools RNASeq
updated 4 months ago by ▴ 210 • written 4 months ago by • 0
2
votes
4
replies
671
views
Does EdgeR trimmed mean of M values (TMM) account for gene length?
Normalization edgeR RNASeq
4 months ago Sabiha ▴ 20
5
votes
7
replies
10k
views
threshold to filter lowly expressed genes
edger rnaseq
updated 4 months ago by • 0 • written 7.2 years ago by • 0
3
votes
1
reply
343
views
Dataset imbalance
RNASeq DifferentialExpression RnaSeqSampleSizeData RnaSeqSampleSize
updated 4 months ago by 50k • written 4 months ago by • 0
5
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7
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1.1k
views
different number of DEG because of outliers
DESeq2 RNASeq
updated 4 months ago by 50k • written 14 months ago by • 0
0
votes
1
reply
294
views
DESeq Design for Time-Series Analysis
RNASeq DESeq2 timecourse
4 months ago WS • 0
3
votes
1
reply
1.8k
views
Is it always preferable to recount library sizes of DGEList object in edgeR after filtering?
edgeR RnaSeqSampleSizeData RNAseq
updated 4 months ago by 50k • written 3.1 years ago by ▴ 60
2
votes
3
replies
1.3k
views
Using STAR's readspergene.tab.out outputs to make gene-level count matrix for DESeq2 using tximport
STAR tximport RNASeq DESeq2
updated 5 months ago by ★ 1.4k • written 5 months ago by • 0
1
vote
2
replies
510
views
How to perform longitudinal analysis using EdgeR
StatisticalMethod FoldChange edgeR RNASeq
5 months ago Sabiha ▴ 20
5
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8
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4.0k
views
Problem about picking soft threshold power in WGCNA software
wgcna rnaseq
written 7.2 years ago by ▴ 40
0
votes
2
replies
1.5k
views
Conducting pair-wise comparison in DESeq2?
DESeq2 deseq2 biocondu Bioconductor RNASeq
written 15 months ago by • 0
50 results • Page 1 of 1
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Replies
Comment: Cannot install oligo on Fedora by mbassal • 0
so whats the solution for this error?
Comment: Why is longestConsecutive() depreceated in version 2.72 (BioC version 3.19)? by ATpoint ★ 4.2k
I don't have an answer to the "why" but maybe a simple reimplemention will do: ```r seqs <- c("ATCATCGTATCAAAGTC", "AAAACGTATCAAAGTC", "TG…
Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by Guido Hooiveld ★ 4.0k
After checking `?DESeqDataSetFromMatrix` note this information: arguments provided to SummarizedExperiment including rowRanges and met…
Answer: Error in gseDO function by Guido Hooiveld ★ 4.0k
Yes, you are missing something. :-) For a GSEA you will need to use as input all genes that you are analyzing; these genes should be ran…
Comment: GSVA function by Robert Castelo ★ 3.3k
No, negative values may occur after log transformation when the `log(x)` is taken from a positive number `x with 0 < x < 1`, and therefore …
Votes
A: Comparison between two different group's pathway analysis results
DiffBind Batch Effect
A: DiffBind Batch Effect
A: DiffBind Batch Effect
C: DiffBind Batch Effect
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