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521 results • Page 1 of 11
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13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 2 days ago by 43k • written 6.8 years ago by ★ 1.3k
5
votes
5
replies
7.2k
views
Converting scRNA-Seq to Bulk-RNASeq
scRNASeq bulk-RNASeq RNA-Seq single-cell
updated 8 days ago by • 0 • written 3.8 years ago by ★ 1.8k
1
vote
3
replies
6.1k
views
Error for converting from gene symbol to Entrez IDs
Entrez-ID org.Dr.eg.db
updated 2 days ago by 43k • written 5.5 years ago by ▴ 170
0
votes
7
replies
6.0k
views
Pre-processing of RNA-Seq data for WGCNA
RNA-Seq WGCNA removeBatchEffect DESeq2
updated 2 days ago by 43k • written 7.6 years ago by ▴ 70
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 9 days ago by • 0 • written 4.7 years ago by ▴ 180
11
votes
22
replies
4.1k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 9 days ago by 43k • written 5.0 years ago by ▴ 260
1
vote
3
replies
4.1k
views
Evaluating removing batch effect tools with PCA or MDS?
bioconductor limma sva r batch-effect
updated 21 hours ago by 43k • written 7.6 years ago by ★ 1.2k
3
votes
6
replies
4.1k
views
how do Differential gene expression analysis by Salmon output
differential-gene-expression Salmon
updated 9 days ago by 43k • written 5.5 years ago by ▴ 100
5
votes
8
replies
3.6k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 9 days ago by 43k • written 6.5 years ago by ★ 1.6k
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling samtools VCF BCF
updated 24 days ago by 43k • written 5.5 years ago by ▴ 110
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 21 hours ago by 43k • written 7.1 years ago by ▴ 310
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 1 day ago by 43k • written 7.0 years ago by ▴ 20
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 2 days ago by 43k • written 7.4 years ago by • 0
0
votes
3
replies
3.0k
views
Rna-seq for differential expression analysis
differential-expression transcriptome
updated 21 hours ago by 43k • written 8.9 years ago by • 0
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq batch-effect sequencing
updated 21 hours ago by 43k • written 6.9 years ago by • 0
0
votes
0
replies
2.8k
views
TCGA RNAseqVer2 batch effects
TCGA RNA-Seq batch-effect
updated 2 days ago by 43k • written 8.5 years ago by • 0
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma RNA-Seq edgeR batch-effect
updated 21 hours 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 1 day 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 1 day ago by 43k • written 6.2 years ago by ▴ 40
0
votes
4
replies
2.7k
views
MACS2 BAMPE and BEDPE gave dramatically different "mean fragment size"
ChIP-Seq
updated 25 days ago by • 0 • written 6.5 years ago by • 0
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca ruvseq sva svaseq batch-effect
updated 2 days ago by 43k • written 6.2 years ago by ▴ 40
5
votes
7
replies
2.7k
views
DESeq2 for differential gene expression on GTEx dataset
differential-gene-expression RNA-Seq GTex DESeq2
updated 9 days ago by 43k • written 6.4 years ago by ▴ 10
0
votes
0
replies
2.7k
views
Comparing lists generated by Counter() and .most_common() for AA seqs
python amino-acid
updated 2 days ago by 43k • written 9.9 years ago by ★ 2.7k
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression RNA-Seq DESeq2
updated 9 days ago by 43k • written 8.0 years ago by ▴ 80
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 2 days ago by 43k • written 6.7 years ago by • 0
0
votes
0
replies
2.4k
views
Filtering using TLOD score in MuTect2?
RNA-Seq Somatic-Mutation Variant-Calling
updated 24 days ago by 43k • written 6.2 years ago by ▴ 600
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect omniexpress GWAS GSA
updated 1 day ago by 43k • written 4.8 years ago by ▴ 10
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq combat rna-seq sva batch-effect
updated 2 days ago by 43k • written 21 months ago by ▴ 20
4
votes
7
replies
2.3k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 10 days ago by 43k • written 3.7 years ago by ▴ 20
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq batch-effect Random-Forest
updated 1 day ago by 43k • written 4.7 years ago by ▴ 10
0
votes
0
replies
2.1k
views
betweenLaneNormalization and calcNormFactors in RUVs
Differential-Gene-Expression RUVs RNA-Seq R
updated 9 days ago by 43k • written 6.8 years ago by ▴ 10
0
votes
5
replies
2.0k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq batch-effect normalization
updated 2 days ago by 43k • written 20 months ago by ▴ 60
1
vote
3
replies
2.0k
views
psmc bootstrapping help
bootstrap psmc
updated 25 days ago by • 0 • written 3.2 years ago by ▴ 50
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect RNA-Seq ARSyNseq limma NOISeq
updated 21 hours ago by 43k • written 6.9 years ago by • 0
0
votes
0
replies
1.9k
views
Correcting batch effect from known variables in RnBeads using Combat
Combat 450k methylation RnBeads batch-effect
updated 21 hours ago by 43k • written 7.1 years ago by ▴ 40
0
votes
0
replies
1.9k
views
batch effect in radseq
radseq batch-effect SNP
updated 21 hours ago by 43k • written 7.4 years ago by ▴ 50
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS exome-sequencing batch-effect
updated 21 hours ago by 43k • written 6.5 years ago by ▴ 270
0
votes
0
replies
1.8k
views
How to get Gene Co-expression Network from RNA seq data using cor() function?
RNA-Seq gene-expression-matrix correlation R
updated 2 days ago by 43k • written 6.3 years ago by ▴ 30
2
votes
0
replies
1.8k
views
ComBat-seq adjustment of batch effects
RNA-Seq ComBat-seq SVA edgeR batch-effect
updated 2 days ago by 43k • written 3.4 years ago by ▴ 50
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat CNA Batch-Effect
updated 1 day ago by 43k • written 5.5 years ago by ▴ 150
0
votes
1
reply
1.8k
views
Advice required for remove batch effect which perfectly collinear with contrast of interest
RNA-seq batch-effect
updated 21 hours ago by 43k • written 6.6 years ago by ▴ 80
0
votes
5
replies
1.8k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing illumina
updated 10 days ago by 3.2k • written 3.4 years ago by • 0
1
vote
0
replies
1.8k
views
Using SVA with RRBS data
sva batch-effect RRBS
updated 2 days ago by 43k • written 7.1 years ago by ▴ 50
0
votes
4
replies
1.8k
views
Correcting batch effect in unevenly distributed groups
RNA-Seq batch-effect R
updated 1 day ago by 43k • written 4.8 years ago by ▴ 20
0
votes
0
replies
1.7k
views
Accounting for hidden batch effects in differential expression analysis with DEXseq and Slueth
Batch-effect RNA-Seq Differential-Expression
updated 2 days ago by 43k • written 7.1 years ago by ▴ 270
0
votes
0
replies
1.7k
views
Differential expression using Scran batch corrected data
single-cell Batch-effect RNA-Seq Scran
updated 21 hours ago by 43k • written 5.4 years ago by ▴ 10
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 2 days ago by 43k • written 2.9 years ago by ▴ 60
1
vote
3
replies
1.7k
views
Using Nanoplot to asses quality of ONT data
ONT Long-read-sequencing NanoPlot
updated 13 days ago by 43k • written 2.2 years ago by ▴ 10
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma Batch-effect MDS Galaxy
updated 2 days ago by 43k • written 4.8 years ago by • 0
1
vote
1
reply
1.7k
views
sea corrected expression matrix
sva microarrays batch-effect
updated 2 days ago by 43k • written 6.8 years ago by ▴ 380
521 results • Page 1 of 11
Recent Votes
Answer: Illumina Read Stitching
Answer: Problem with Sniffles pipeline and SV calling help
Illumina reads preprocessing best practice for snp calling applications
Comment: Illumina reads preprocessing best practice for snp calling applications
Installing/switching between versions of R/Rstudio/Bioconductor
How To Generate Phylogeny Tree, Based On Snps?
How To Construct Phylogenetic Tree Using Snps
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Recent Replies
Comment: Installing/switching between versions of R/Rstudio/Bioconductor by Ram 43k
Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
Comment: Should I apply doublet detection for each pool seperately? by Ram 43k
Do not delete posts that have received feedback,
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues by _quantum_girl_ ▴ 10
They aren't merging any datasets. Just for reference the paper is this: https://www.nature.com/articles/s41380-022-01674-9#MOESM1. Citing: …
Comment: RNA seq differential expression analysis by BioinfGuru ★ 1.7k
https://help.galaxyproject.org/
Answer: RNA seq differential expression analysis by Mohamed Abderrahmane ▴ 10
The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.
Comment: Illumina reads preprocessing best practice for snp calling applications by Enrique • 0
Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
Comment: Could you please assist in identifying this cluster? by ATpoint 81k
The information do not suffice. Please show plots and identified marker genes. Also, make sure it is not a trash cluster with low number of…
Comment: Free/open source 23andme-like analysis by joe ▴ 510
Thank you, I added 'accurate' now ;) I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this infor…
Comment: Memory usage of picard Samsort by ATpoint 81k
Guys, just use `samtools sort` which won't get you into trouble with any of that.
Comment: Ciriquant not configuring hisat2 indexed files by Carlo Yague 8.6k
I don't know for sure, but I think that decreasing the amount of threads (1 or 2 instead of 4) will decrease the memory requirements of the…
Answer: Memory usage of picard Samsort by tamas.malkocs • 0
For me, setting `TMP_DIR` (`--TMP_DIR /home/tmp`) didn't work in picard 2.21.1. What solved the issue was setting the environmental variabl…
Answer: Plink merge errors. by Dinmukhamed • 0
I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files by Atul K. • 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file by Maria • 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis by Michael 54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
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