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85
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24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 15 hours ago by • 0 • written 3.5 years ago by 3.2k
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 3 hours ago by 6.3k • written 10.9 years ago by ▴ 10
23
votes
23
replies
9.7k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq removeBatchEffect batch-effect edger
updated 23 hours ago by 43k • written 5.3 years ago by ▴ 130
11
votes
9
replies
6.9k
views
How to choose method to integrate different patient sample together in Seurat
Seurat scRNA batch-effect harmony
updated 23 hours ago by 43k • written 4.2 years ago by ▴ 80
7
votes
3
replies
4.5k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 23 hours ago by 43k • written 5.1 years ago by ▴ 100
2
votes
4
replies
4.5k
views
Differential Expression Analysis with monocle and batch effect correction
single-cell RNA-Seq batch-effect
updated 23 hours ago by 43k • written 5.9 years ago by ▴ 60
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 23 hours ago by 43k • written 4.9 years ago by ▴ 330
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq batch-effect
updated 23 hours ago by 43k • written 4.7 years ago by ▴ 30
7
votes
5
replies
3.5k
views
ISCN annotation for SV/CN VCF files
SV
updated 13 hours ago by • 0 • written 7 months ago by ▴ 50
1
vote
8
replies
3.4k
views
Best way to address different batches of RNA-seq
sequence RNA-Seq RPKM Fold-Change batch-effect
updated 23 hours ago by 43k • written 7.0 years ago by ▴ 20
2
votes
1
reply
3.1k
views
Batch effect correction in DE analysis of single cell RNA-seq data and visualization
Seurat Batch-effect SCDE RNA-Seq Limma
updated 23 hours ago by 43k • written 5.5 years ago by ▴ 60
0
votes
2
replies
2.9k
views
Should I pre-normalize RNAseq data before combat?
RNA-Seq combat batch-effect R
updated 23 hours ago by 43k • written 4.8 years ago by ▴ 50
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq RNA-Seq batch-effect DESeq2
updated 23 hours ago by 43k • written 5.1 years ago by ★ 2.6k
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva batch-effect
updated 21 hours ago by 43k • written 6.2 years ago by ▴ 40
4
votes
4
replies
2.6k
views
Advice on Handling Batch Effect in ChIP-seq Experiment
ChIP-Seq batch-effect sequencing
updated 23 hours ago by 43k • written 4.6 years ago by ▴ 20
8
votes
6
replies
2.5k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 19 hours ago by 3.0k • written 23 months ago by ▴ 230
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect omniexpress GWAS GSA
updated 23 hours ago by 43k • written 4.8 years ago by ▴ 10
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq batch-effect Random-Forest
updated 23 hours ago by 43k • written 4.7 years ago by ▴ 10
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 3 hours ago by 43k • written 4.8 years ago by ▴ 20
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq tophat batch-effect cufflinks
updated 23 hours ago by 43k • written 5.3 years ago by • 0
1
vote
2
replies
2.1k
views
RNA-seq unbalanced batch effect correction
RNA-Seq edgeR R Batch-Effect
updated 23 hours ago by 43k • written 5.6 years ago by ▴ 730
3
votes
5
replies
2.1k
views
DE analysis with edgeR and possibly batch effect
analysis edgeR batch-effect DE
updated 23 hours ago by 43k • written 5.1 years ago by ★ 1.9k
2
votes
5
replies
1.9k
views
Differential Expression Analysis with batches which have different biological groups
R RNA-Seq limma DE batch-effect
updated 23 hours ago by 43k • written 4.8 years ago by ▴ 60
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression TPM RNA-Seq counts batch-effect
23 hours ago by Ram 43k
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat CNA Batch-Effect
updated 23 hours ago by 43k • written 5.4 years ago by ▴ 150
0
votes
4
replies
1.7k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq batch-effect R
updated 23 hours ago by 43k • written 4.8 years ago by ▴ 20
2
votes
2
replies
1.7k
views
Remove batch effect for many RNA-seq
ComBat RNA-Seq batch-effect sva
updated 23 hours ago by 43k • written 4.8 years ago by • 0
0
votes
0
replies
1.7k
views
Batch effect and CCA
CCA RNA-Seq seurat batch-effect
updated 23 hours ago by 43k • written 5.1 years ago by ▴ 110
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 23 hours ago by 43k • written 4.7 years ago by ▴ 60
0
votes
2
replies
1.3k
views
Interpretation problem at PCA plot for detecting batch effect
PCA RNA-Seq batch-effect
updated 23 hours ago by 43k • written 4.4 years ago by ▴ 170
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray meta-analysis DEG batch-effect
updated 23 hours ago by 43k • written 4.8 years ago by ▴ 30
0
votes
1
reply
1.3k
views
About BatchQC packages error
Batch-effect R
updated 23 hours ago by 43k • written 6.0 years ago by • 0
1
vote
1
reply
1.3k
views
Can we use previous estimated ComBat model to correct batch effects for new data?
microarray RNA-Seq batch-effect
updated 23 hours ago by 43k • written 5.0 years ago by ▴ 160
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq batch-effect DESeq2
updated 23 hours ago by 43k • written 4.4 years ago by ▴ 10
0
votes
1
reply
1.2k
views
Controlling for batch effect in SNP-based PCA
whole-genome PCA batch-effect SNP
updated 23 hours ago by 43k • written 4.7 years ago by ▴ 90
1
vote
9
replies
1.1k
views
Supergnova stuck in tutorial
Genetic Correlations Python Supergnova Conda
updated 7 hours ago by • 0 • written 19 months ago by ▴ 10
0
votes
0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect scRNA-seq feature-selection
updated 23 hours ago by 43k • written 4.9 years ago by ▴ 140
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat RNA-Seq batch-effect
updated 23 hours ago by 43k • written 4.3 years ago by ▴ 360
0
votes
1
reply
825
views
How to compare differentially expressed genes among different affymatrix dataset
microarray batch-effect R
updated 23 hours ago by 43k • written 4.8 years ago by ▴ 30
2
votes
6
replies
546
views
Removing duplicates
duplicates ONT minimap2
9 hours ago by quentinperriere • 0
3
votes
1
reply
539
views
What is the normalization status of metabric data?
metabric normalization microarray cbioportal
updated 17 hours ago by ▴ 20 • written 19 months ago by ★ 4.3k
1
vote
9
replies
529
views
How can I retrieve wheat lysine non-acetylated sequences from the UniProt database?
UniProt
updated 4 hours ago by ★ 2.4k • written 9 hours ago by • 0
1
vote
4
replies
491
views
What happened to Tombo Re-squiggle
Tombo resquiggle ONT
updated 2 hours ago by 43k • written 3 months ago by • 0
1
vote
10
replies
465
views
Questions about a bug when transferring cram file to bam file
sequence samtools bcftools
updated 2 hours ago by 141k • written 1 day ago by • 0
2
votes
3
replies
379
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
updated 21 hours ago by 14k • written 1 day ago by ★ 1.7k
0
votes
4
replies
380
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx deconcolution
10 hours ago by feather-W • 0
0
votes
1
reply
351
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree microbiome
updated 3 hours ago by 43k • written 19 months ago by • 0
1
vote
4
replies
299
views
SLURM submission problem: Indexing the Reference Genome is not done in STAR
align RNA-Seq linux STAR
updated 5 hours ago by 141k • written 9 hours ago by • 0
3
votes
4
replies
297
views
biomaRt error for different R version
biomaRt R
updated 5 hours ago by 141k • written 1 day ago by ▴ 490
2
votes
3
replies
290
views
Sheep reference genome remapping coordinates
reference remap sheep coordinates genome
4 hours ago by valentinatsar • 0
79 results • Page 1 of 2
Recent Votes
Exporting WGCNA step-to-step network construction objects into igraph object
Comment: Downloaded pdb's on rcsb.org
Answer: How to compare the quality of assemblies
How to compare the quality of assemblies
A: Best strategy for gene annotation for de novo genome assembly without RNA-seq da
Comment: Questions about a bug when transferring cram file to bam file
Answer: Problem with Mirdeep2 and Randfold output
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Commentator to GenoMax 141k
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Recent Replies
Comment: Downloaded pdb's on rcsb.org by GenoMax 141k
Download services for PDB are described on this page: https://www.rcsb.org/docs/programmatic-access/file-download-services It could be as …
Answer: How to compare the quality of assemblies by shelkmike ★ 1.2k
Since BUSCO results are almost identical but the assembly sizes differ significantly, I suppose that the difference between the assemblies …
Comment: differential gene expression analysis when not all samples have an untreated cou by nhaus ▴ 300
Thank you very much for your answer, that was very helpful! > Impossible to say. It depends on your data, particularly on how the donors …
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues by bk11 ★ 2.3k
This could be because they are probably merging two or more datasets. If you are merging two or more datasets, it will be very important th…
Answer: Problem with Mirdeep2 and Randfold output by otieno43 ▴ 30
I sorted this out by first removing white space in the first line of the reference genome. Then indexed, the ran the mapper.pl script follo…
Comment: Questions about a bug when transferring cram file to bam file by GenoMax 141k
Just to be certain, you are saying that if OP runs `samtools view` without the explicit reference it will be automatically downloaded from …
Comment: Questions about a bug when transferring cram file to bam file by jkbonfield ★ 1.2k
That SQ M5 is chr1 in my copy of GRCh38 (Homo_sapiens.GRCh38_full_analysis_set_plus_decoy_hla.fa). I'm assuming your hg38.fa is not the sa…
Comment: What happened to Tombo Re-squiggle by Ram 43k
Please do not add answers unless you're answering the top level question. Instead, use `Add Comment` or `Add Reply` as appropriate. I've mo…
Comment: What happened to Tombo Re-squiggle by Joseph • 0
Hi, Does anybody has the answer to this? I also want to resquiggle my data with Remora but do not quite get which is the appropriate com…
Comment: How To Identify The 16S Rrna Gene Sequence In A Genome by colindaven 6.3k
It's also worth mentioning `Barrnap` is in the bacterial annotation system **Prokka**. `Prokka` can be installed on Debian systems with `…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by Elisabeth Gasteiger ★ 2.4k
See also https://www.uniprot.org/help/negative_datasets
Comment: Sheep reference genome remapping coordinates by valentinatsar • 0
Thank you for your response As I can understand this tool takes sequence input files right? I have genome-wide genotypes instead of sequen…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by me ▴ 750
Ok I made this into an answer. Could you please accept it as such.
Answer: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa by me ▴ 750
You can't. The data does not exist. UniProt only annotates where a lysine is know to be acetylated. There is no way that UniProt can know w…
Comment: How to compare the quality of assemblies by GenoMax 141k
Are there any short read datasets available in SRA? Can you try and see how many left over reads remain after you align to both of your ass…
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