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1,101 results • Page 3 of 23
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1
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3
replies
3.4k
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How to correct for batch effect in microarray meta-analysis
ComBat microarray meta-analysis batch-effect
updated 13 days ago by 43k • written 10.0 years ago by ▴ 120
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 15 days ago by 43k • written 5.3 years ago by ▴ 120
3
votes
4
replies
3.3k
views
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
next-gen
updated 20 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 22 days ago by 43k • written 7.9 years ago by • 0
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat R SVA Biostatistics batch-effect
updated 13 days ago by 43k • written 7.4 years ago by • 0
0
votes
1
reply
3.2k
views
Removing batch effects from RPKM data
limma removeBatchEffect batch-effect rpkm
updated 15 days ago by 43k • written 8.5 years ago by ▴ 360
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq batch-effect
updated 13 days ago by 43k • written 7.1 years ago by ▴ 40
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 14 days ago by 43k • written 5.5 years ago by ▴ 60
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression transcriptome
updated 13 days ago by 43k • written 9.0 years ago by • 0
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq batch-effect sequencing
updated 13 days ago by 43k • written 7.0 years ago by • 0
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression RNA-seq
updated 22 days ago by 43k • written 6.5 years ago by ★ 1.6k
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor batch-effect
updated 13 days ago by 43k • written 7.9 years ago by ★ 3.4k
0
votes
2
replies
3.0k
views
Should I pre-normalize RNAseq data before combat?
RNA-Seq combat batch-effect R
updated 14 days ago by 43k • written 4.8 years ago by ▴ 50
1
vote
2
replies
2.9k
views
Taking surrogate variable into account before running PCA
sva svaseq batch-effect
updated 13 days ago by 43k • written 6.9 years ago by • 0
0
votes
1
reply
2.9k
views
Microarray batch effect correction
Microarray Batch-effect
updated 13 days ago by 43k • written 6.7 years ago by ▴ 100
7
votes
3
replies
2.9k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 13 days ago by 6.4k • written 16 months ago by ▴ 130
0
votes
0
replies
2.8k
views
TCGA RNAseqVer2 batch effects
TCGA RNA-Seq batch-effect
updated 15 days ago by 43k • written 8.6 years ago by • 0
2
votes
5
replies
2.8k
views
Batch effect in Axiom Human Origins Array
affymetrix array batch-effect
updated 15 days ago by 43k • written 7.9 years ago by ▴ 50
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq breast cancer subtyping
updated 15 days ago by ▴ 70 • written 5.7 years ago by ▴ 50
1
vote
5
replies
2.8k
views
Batch effect identification using PCA
PCA qRT-PCR R targeted-assay Batch-Effect
updated 16 days ago by 43k • written 3.9 years ago by ▴ 250
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma RNA-Seq edgeR batch-effect
updated 13 days ago by 43k • written 7.0 years ago by • 0
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq RNA-Seq batch-effect DESeq2
updated 14 days ago by 43k • written 5.1 years ago by ★ 2.6k
1
vote
1
reply
2.8k
views
removing batch effects from large number of data sets
Microarray batch-effect
updated 15 days ago by 43k • written 5.9 years ago by ▴ 520
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva batch-effect
updated 14 days ago by 43k • written 6.2 years ago by ▴ 40
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma gwas
updated 2 days ago by • 0 • written 4.9 years ago by ▴ 90
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 7 days ago by • 0 • written 8.3 years ago by • 0
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 22 days ago by 43k • written 6.4 years ago by ▴ 10
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca ruvseq sva svaseq batch-effect
updated 15 days ago by 43k • written 6.2 years ago by ▴ 40
7
votes
10
replies
2.7k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch batch-effect DESeq2 rna-seq
updated 15 days ago by 43k • written 2.0 years ago by ▴ 60
2
votes
5
replies
2.7k
views
primer design to discriminate sequences in intron-exon MSA
primer MSA intron-exon
updated 26 days ago by • 0 • written 6.6 years ago by ▴ 630
3
votes
16
replies
2.7k
views
design matrix for dge
limma differential-gene-expression r
updated 22 days ago by 43k • written 7.9 years ago by ▴ 50
0
votes
0
replies
2.7k
views
Comparing lists generated by Counter() and .most_common() for AA seqs
python amino-acid
updated 15 days ago by 43k • written 9.9 years ago by ★ 2.7k
4
votes
9
replies
2.7k
views
Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.3 years ago by • 0
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression RNA-Seq DESeq2
updated 22 days ago by 43k • written 8.1 years ago by ▴ 80
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 13 days ago by 43k • written 9.1 years ago by ▴ 110
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 14 days ago by 3.0k • written 24 months ago by ▴ 230
4
votes
4
replies
2.6k
views
Advice on Handling Batch Effect in ChIP-seq Experiment
ChIP-Seq batch-effect sequencing
updated 14 days ago by 43k • written 4.6 years ago by ▴ 20
2
votes
4
replies
2.6k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel gatk calling snp variant
updated 2 days ago by 9.7k • written 24 months ago by ▴ 120
0
votes
0
replies
2.6k
views
Removing batch effects from methylation beta values for molecular subtyping/cluster analysis
clustering beta-values batch-effect methylation
updated 15 days ago by 43k • written 6.7 years ago by • 0
6
votes
0
replies
2.6k
views
Tool: Immuno-Navigator, a batch-corrected database for gene coexpression in the immune system
gene-co-expression batch-effect immunology
updated 13 days ago by 43k • written 7.0 years ago by ▴ 80
0
votes
9
replies
2.5k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome base-calling fastq nanopore
updated 3 days ago by 43k • written 8 months ago by • 0
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA batch-effect gene-expression
updated 23 days ago by 43k • written 3.5 years ago by ▴ 240
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink PED
updated 9 days ago by 10k • written 6.1 years ago by ▴ 10
0
votes
1
reply
2.4k
views
Job: Full Stack Web Developer - Cambridge, UK
JavaScript Python Visualisation
written 8.4 years ago by ▴ 400
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq combat rna-seq sva batch-effect
updated 15 days ago by 43k • written 21 months ago by ▴ 20
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect omniexpress GWAS GSA
updated 14 days ago by 43k • written 4.8 years ago by ▴ 10
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi metagenomics centrifuge gi_taxid_nucl.dmp taxonomy
updated 7 days ago by • 0 • written 2.4 years ago by • 0
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 23 days ago by 43k • written 3.7 years ago by ▴ 20
1
vote
5
replies
2.4k
views
Shannon vs Simpson for TCR diversity estimation
TCR shannon simpson
updated 20 days ago by 82k • written 5.1 years ago by ▴ 750
3
votes
3
replies
2.4k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 6 days ago by • 0 • written 22 months ago by ▴ 180
1,101 results • Page 3 of 23
Recent Votes
Answer: Bacterial plasmid analysis
Answer: Bacterial plasmid analysis
Discrepancy in read counts from fastq
R: Unable to use analyzeFeatures because argument is not a vector
Comment: Odd alignment question/finding
Comment: POSSUM not working due to incompatible pssm file
Comment: Can't install AnnotationHub
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Recent Replies
Answer: Subsetting and merging back Seurat Object brings different results by Bine ▴ 60
Noone has an idea? Thank you!
Answer: Bacterial plasmid analysis by shenwei356 8.5k
My colleague has an unpublished tool for plasmid analysis (clustering), and it has really good results. You might have a try. https://githu…
Comment: Odd alignment question/finding by ATpoint 82k
bwa mem is not fully deterministic, see from the developer: https://www.biostars.org/p/238628/#238817
Comment: How to perform single cell multimodal integration using Seurat for Geo datasets by ATpoint 82k
It's funny that you ask because the paper that these data were used for is called `Integrated analysis of multimodal single-cell data` from…
Comment: Odd alignment question/finding by liorglic ★ 1.4k
I can't come up with an explanation, but two things you can try for debugging are: 1) look at the fastp stats - do they add up and make sen…
Answer: Bacterial plasmid analysis by Mensur Dlakic ★ 27k
If you put all your sequences in separate files but in the same directory, this program will build a cladogram based on average nucleotide …
Comment: POSSUM not working due to incompatible pssm file by rianna.collins • 0
Thank you so much. I'm new to this and didn't realise there was a code option.
Answer: Is there a way to increase the automatic label text size in Cytoscape? by Scooter ▴ 280
Greetings, Are you saying that you can't use the size setting in the style tab? That should certainly work, as should the label size se…
Answer: Basic stats in hierfstat by mdav • 0
Hi Zoe, did you find an answer for this? I am also getting the same error.
Comment: GATK won't produce figures while analyzing covariates to generate 'recal_plots.p by GenoMax 141k
Your cluster may be missing libraries etc to create the PDF plots (this looks like a cluster job submission) on your cluster. Did you check…
Comment: Post-imputation plot by kl ▴ 10
Ok yes I think my thought was that given these errors, I could remove the mismatches and flip the alleles which seem to need flipping based…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
I think I will perhaps use their predominant PlasmidFinder type to group plasmids together and create separate core phylogenies for each as…
Comment: Bacterial plasmid analysis by GenoMax 141k
Can you classify the plasmids based on function (resistance genes they are carrying or some other criteria). Sizes above are indicating a w…
Comment: DESeq2 processing problems by ATpoint 82k
Initially posted here https://support.bioconductor.org/p/9158036/ where I suggested to put code and data and noted that GEOquery returns ar…
Answer: Post-imputation plot by LChart 3.9k
I agree that some need to be flipped (A/T and C/G where your panel frequency is 1 - ref panel frequency). There are other variants which yo…
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