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266 results • Page 1 of 6
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85
votes
23
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 2 days ago by • 0 • written 3.5 years ago by 3.2k
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression RNAseq heatmap
updated 6 days ago by 43k • written 4.7 years ago by ▴ 370
37
votes
5
replies
13k
views
How do you generate TMM normalized counts using EdgeR?
R RNA-seq edgeR
updated 5 days ago by ▴ 60 • written 2.8 years ago by ★ 1.0k
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato gene
updated 5 days ago by • 0 • written 8.8 years ago by ▴ 170
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly statistics
updated 2 days ago by • 0 • written 4.7 years ago by ▴ 10
5
votes
13
replies
9.0k
views
8 follow
biomaRt: Timeout on getBM().
r biomart ensembl
updated 4 days ago by ★ 2.0k • written 2.8 years ago by ▴ 40
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 5 days ago by • 0 • written 3.8 years ago by ★ 1.8k
13
votes
10
replies
6.3k
views
Adjusting for confounding variables in RNA-SEQ Differential Expression Analysis
Differential-Gene-Expression RNA-Seq Statistics
updated 6 days ago by 43k • written 5.7 years ago by ▴ 40
7
votes
20
replies
6.3k
views
7 follow
Repeat masked gtf files from ensembl
ensembl RNA-Seq genome
updated 4 days ago by ▴ 190 • written 4.3 years ago by ▴ 80
0
votes
8
replies
5.2k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 6 days ago by • 0 • written 4.7 years ago by ▴ 180
3
votes
2
replies
5.2k
views
RNASeq: Differential gene expression and qqplot
limma differential-gene-expression RNA-Seq deseq2
updated 6 days ago by 43k • written 6.1 years ago by ★ 1.6k
2
votes
7
replies
5.1k
views
9 follow
problem with HOMER findMotifsGenome.pl
HOMER ATAC-Seq
updated 5 days ago by • 0 • written 5.5 years ago by ▴ 80
1
vote
7
replies
5.0k
views
How do I plot several sns.clustermap heatmaps in a single figure?
python seaborn
updated 5 days ago by ▴ 40 • written 3.4 years ago by ▴ 880
0
votes
1
reply
5.0k
views
How to compute a one tail (one way) log rank test for survival?
R survival hypothesis-testing log-rank
updated 5 days ago by • 0 • written 7.5 years ago by ▴ 30
18
votes
20
replies
4.3k
views
6 follow
How to identify significant differentially expressed genes and gene regulatory networks from microarray data.
microarray differential-gene-expression
updated 6 days ago by 43k • written 7.5 years ago by ▴ 80
12
votes
13
replies
4.3k
views
RNA-Seq DGE using PCA components as covariate
differential-gene-expression RNA-Seq glm DESeq2
updated 6 days ago by 43k • written 6.2 years ago by ★ 1.6k
6
votes
6
replies
4.3k
views
10x to cloupe
single-cell-transcriptomics 10x
6 days ago by firestar ★ 1.6k
5
votes
20
replies
4.1k
views
Differential gene expression from RNAseq data. Before or after annotation?
differential-gene-expression RNA-seq
updated 6 days ago by 43k • written 6.2 years ago by ▴ 90
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 6 days ago by 43k • written 5.0 years ago by ▴ 260
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 6 days ago by 43k • written 5.5 years ago by ▴ 100
1
vote
10
replies
3.8k
views
Error in CIBERSORTx
RNA-seq CIBERSORT LM22
updated 1 day ago by ▴ 300 • written 18 months ago by • 0
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 14 hours ago by 43k • written 4.0 years ago by ▴ 330
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 6 days ago by 43k • written 6.5 years ago by ★ 1.6k
3
votes
4
replies
3.3k
views
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
next-gen
updated 4 days ago by 43k • written 6.7 years ago by ▴ 10
1
vote
3
replies
3.3k
views
How to calculate Differential Gene expression between samples with replicates
Differential-Gene-Expression RNA-Seq
updated 6 days ago by 43k • written 7.8 years ago by • 0
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression RNA-seq
updated 6 days ago by 43k • written 6.5 years ago by ★ 1.6k
1
vote
5
replies
2.8k
views
Batch effect identification using PCA
PCA qRT-PCR R targeted-assay Batch-Effect
updated 14 hours ago by 43k • written 3.8 years ago by ▴ 250
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 6 days ago by 43k • written 6.4 years ago by ▴ 10
3
votes
16
replies
2.6k
views
design matrix for dge
limma differential-gene-expression r
updated 6 days ago by 43k • written 7.9 years ago by ▴ 50
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression RNA-Seq DESeq2
updated 6 days ago by 43k • written 8.0 years ago by ▴ 80
1
vote
5
replies
2.3k
views
Shannon vs Simpson for TCR diversity estimation
TCR shannon simpson
updated 4 days ago by 81k • written 5.0 years ago by ▴ 750
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma microarray differential-gene-expression
updated 6 days ago by 43k • written 6.1 years ago by ▴ 170
2
votes
5
replies
2.3k
views
DGE on transcriptomic data, focus on transcript sequences or in derivated ORFs?
differential-gene-expression RNA-Seq ORFs
updated 6 days ago by 43k • written 6.4 years ago by ▴ 90
9
votes
5
replies
2.2k
views
Millions of Reads Needed for Differential Gene Expression
differential-gene-expression RNA-Seq deseq2
updated 6 days ago by 43k • written 4.5 years ago by ▴ 20
5
votes
4
replies
2.2k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts DESEQ2 differential-gene-expression kallisto
updated 6 days ago by 43k • written 2.7 years ago by ▴ 170
3
votes
1
reply
2.1k
views
Maximum Number of Gene in a DESeq2 and edgeR
Differential-Gene-Expression EdgeR DESeq2
updated 6 days ago by 43k • written 8.0 years ago by ▴ 10
2
votes
5
replies
2.1k
views
Generating a heatmap in DEG analysis
Differential-gene-expression RNA-Seq
updated 6 days ago by 43k • written 3.1 years ago by ▴ 10
0
votes
0
replies
2.1k
views
betweenLaneNormalization and calcNormFactors in RUVs
Differential-Gene-Expression RUVs RNA-Seq R
updated 6 days ago by 43k • written 6.8 years ago by ▴ 10
1
vote
6
replies
2.0k
views
DGE on protein-coding and lncRNAs separately?
differential-gene-expression RNA-seq
updated 6 days ago by 43k • written 6.4 years ago by ★ 1.6k
4
votes
6
replies
2.0k
views
RNA-Seq DGE: Evaluate model quality
differential-gene-expression RNA-Seq deseq2
updated 6 days ago by 43k • written 6.2 years ago by ★ 1.6k
0
votes
4
replies
1.9k
views
Requesting help with RNA-Seq differential gene analysis
differential-gene-expression deseq2
updated 6 days ago by 43k • written 6.2 years ago by ▴ 50
0
votes
0
replies
1.9k
views
Job: Bioinformatics Research Postdoc
RNA-Seq genome
updated 4 days ago by 43k • written 8.2 years ago by • 0
4
votes
5
replies
1.9k
views
which package should be selected for differential gene expression analysis
Differential-gene-expression RNA-Seq
updated 6 days ago by 43k • written 5.5 years ago by ▴ 100
0
votes
5
replies
1.8k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing illumina
updated 6 days ago by 3.2k • written 3.4 years ago by • 0
2
votes
2
replies
1.7k
views
EdgeR in Galaxy. Adjust C-value?
Differential-gene-expression EdgeR Galaxy C-value
updated 6 days ago by 43k • written 7.6 years ago by ▴ 60
0
votes
0
replies
1.7k
views
Differential Gene Expression Analysis using two distinct scRNA-seq datasets
differential-gene-expression RNA-Seq scRNA-seq
updated 6 days ago by 43k • written 6.5 years ago by ▴ 120
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma sva batch-effect R
updated 14 hours ago by 43k • written 3.8 years ago by ▴ 10
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq edgeR batch-effect
updated 14 hours ago by 43k • written 3.8 years ago by ▴ 20
3
votes
6
replies
1.5k
views
edgeR FDR always 1
FDR differential-gene-expression edgeR miRNA
updated 6 days ago by 43k • written 4.8 years ago by ▴ 10
2
votes
3
replies
1.5k
views
Duplicate row name not allowed while reading the file in R
RNA-Seq deseq2 Differential-Gene-expression R
updated 6 days ago by 43k • written 4.8 years ago by • 0
266 results • Page 1 of 6
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Comment: How does FindNeighbors() and FindClusters() related and work?
Answer: Deseq2 : Paired analysis or otherwise
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Recent Replies
Comment: Ensembl gene id conversion by naveedhasan2000 • 0
I actually have a list of ensembl ids generated while doing a read count using htseq, i used the reference genome from ensembl. I then trie…
Comment: Odd results with BLAST remote by b.contreras.moreira ▴ 150
See https://www.biostars.org/p/9486493 and parameter `-max_hsps 1`
Answer: WGCNA network from Adjacency or TOM matrix by andres.firrincieli 3.6k
Since the module detection is performed on the TOM, you should go for the TOM.
Answer: Error in edgeR/Deseq2 Analysis by kuttibiotech2009 ▴ 30
The error message you're encountering suggests that there might be duplicate row names in your input data file. check it once again whether…
Comment: Getting marker genes for cell types by orzrzlyo ▴ 20
Thank you! Also, cell typist would successfully identify the above cell types, however, they seemed to be in a pretrained or pre-organized …
Answer: Getting marker genes for cell types by LChart 3.9k
It seems strange that celltypist would not identify these major cell classes -- you should double check your data quality. For the marker l…
Answer: gene body coverage with RSeqQC by jkim ▴ 170
http://qualimap.conesalab.org/doc_html/index.html Never tried rseqc, but qualimap provides a gene body coverage plot also.
Comment: How to get the reference panel sites for TOPMed hg37 and 38 by bk11 ★ 2.3k
You can simply impute your genotyped data in TOPMed server. In that way you do not have to deal with downloading the reference panels (not …
Answer: Using adonis to include a random effect by LChart 3.9k
> why the first model doesn't have stats for both variables? Your variables are multicollinear. This will always be true if you have mul…
Comment: How to row normalize a matrixplot? by bioinfo ▴ 150
Thank you. That is what I ended up doing.
Comment: bash script by Ram 43k
What "error code at the top" are you talking about? Error code in response to the `srun -N 1 -t 0:01:00 bash -c "uname -a"` command? Also, …
Answer: how to get the variance explained by the independent variable from multivariate by LChart 3.9k
More explicitly: ```R G <- mdmr::gower(distance.matrix) eig <- eigen(G) U <- eig$vectors ## this is the MDS embedding matrix lambd…
Comment: bash script by bestone ▴ 30
You write this "I noticed there may be a few parameters required for a SLURM job that could be missing from your script (partition to use, …
Comment: RNAseq 1 control 2 different treatment by sansan_96 ▴ 70
I think what you should do is do differential expression for your two contrasts: treatment 1 vs control and treatment 2 vs control. DESeq2 …
Comment: how to get the variance explained by the independent variable from multivariate by leranwangcs ▴ 120
Thanks for your response! I have no statistics background so a bit hard to figure our the equation you provide with. I just want to find so…
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