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544 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 7 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 13 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 7 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 7 days ago by 43k • written 7.6 years ago by ▴ 70
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython PDB Radius of Gyration python protein
updated 4 days ago by • 0 • written 6.5 years ago by ▴ 30
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing software-error RNA-seq
updated 14 days ago by • 0 • written 4.7 years ago by ▴ 180
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 15 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 5 days 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 15 days ago by 43k • written 5.5 years ago by ▴ 100
5
votes
8
replies
3.7k
views
Many Differentially expressed genes but few GO terms
differential-gene-expression RNA-seq gene-ontology
updated 15 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 29 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 5 days 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 6 days ago by 43k • written 7.0 years ago by ▴ 20
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 7 days ago by 43k • written 7.4 years ago by • 0
0
votes
3
replies
3.1k
views
Rna-seq for differential expression analysis
differential-expression transcriptome
updated 5 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 5 days 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 7 days ago by 43k • written 8.6 years ago by • 0
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma RNA-Seq edgeR batch-effect
updated 5 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 6 days 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 6 days ago by 43k • written 6.2 years ago by ▴ 40
1
vote
1
reply
2.7k
views
Plotting a PCA Plot from SVASeq results
pca ruvseq sva svaseq batch-effect
updated 7 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 15 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 7 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 15 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 7 days ago by 43k • written 6.7 years ago by • 0
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink PED
updated 1 day ago by 10k • written 6.1 years ago by ▴ 10
0
votes
0
replies
2.4k
views
Filtering using TLOD score in MuTect2?
RNA-Seq Somatic-Mutation Variant-Calling
updated 29 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 6 days 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 7 days ago by 43k • written 21 months ago by ▴ 20
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect DESeq2 combat_seq
updated 16 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 6 days 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 15 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 7 days ago by 43k • written 20 months ago by ▴ 60
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect RNA-Seq ARSyNseq limma NOISeq
updated 5 days 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 5 days 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 5 days ago by 43k • written 7.5 years ago by ▴ 50
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS exome-sequencing batch-effect
updated 5 days 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 7 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 7 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 6 days ago by 43k • written 5.5 years ago by ▴ 150
0
votes
5
replies
1.8k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing illumina
updated 15 days ago by 3.2k • written 3.4 years ago by • 0
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 5 days ago by 43k • written 6.6 years ago by ▴ 80
1
vote
0
replies
1.8k
views
Using SVA with RRBS data
sva batch-effect RRBS
updated 7 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 6 days ago by 43k • written 4.8 years ago by ▴ 20
0
votes
0
replies
1.8k
views
Differential expression using Scran batch corrected data
single-cell Batch-effect RNA-Seq Scran
updated 5 days ago by 43k • written 5.4 years ago by ▴ 10
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 7 days ago by 43k • written 7.2 years ago by ▴ 270
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 7 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 18 days ago by 43k • written 2.3 years ago by ▴ 10
1
vote
2
replies
1.7k
views
Batch effects and MDSPlot in limma
limma Batch-effect MDS Galaxy
updated 7 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 7 days ago by 43k • written 6.8 years ago by ▴ 380
544 results • Page 1 of 11
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Recent Replies
Comment: AGeNT LocatIt by barslmn ★ 2.1k
He is already giving 32G, 320G for marking duplicates for exome is excessive. Is there a specific reason for using the tool?
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
This looks good. Please try with using `--allow-no-sex flag` plink --bfile your_data_phenoUP --assoc --allow-no-sex --out your_data_ph…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
SC899359_PC75420_A05 SC899359_PC75420_A05 0 0 0 2 SC899360_PC75415_D01 SC899360_PC75415_D01 0 0 0 2 SC899361_PC75425_H05 SC899361_PC75425_H…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
Please show me a few lines of phenotype updated .fam file. You can do `head your_data_phenoUP.fam` and paste result here. Please do not us…
Comment: GEMMA GWAS how to specify factor or numerical for covariates by Sofia • 0
Hi, I don't have a solution to your question but I followed this tutorial and was helpful to me in my analysis https://youtu.be/NusV6duyvXs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas by GenoMax 141k
Catalog file lists the genomes included. There seem to be 71365 unique items in field 2. 2 Bacteria WP_000018326.1 4459…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
yes sure ! ![enter image description here][1] [1]: /media/images/f0f94f6c-4387-4188-a1aa-19152a89
Answer: AGeNT LocatIt by Greg • 0
Give it more memory. ~10x more memory, or whatever you can give it, I had samples that weren't even close to being done after 3.5 da…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas by Bertalan_Takacs ▴ 90
Thanks! I've already tried looking through these files, I need release 83. I am trying to find this information in the .catalog file of the…
Answer: Is it possible to get a list of representative genomes from a past RefSeq releas by GenoMax 141k
Possibly. You will need to know the RefSeq release version. Check in this directory: https://ftp.ncbi.nlm.nih.gov/refseq/release/release-ca…
Comment: How to convert plink files to Hapmap Format by bk11 ★ 2.3k
Hey, can you please show me a few lines of your phenotype updated .fam file? I m seeing there are 7 columns in it, that might be the proble…
Comment: PCA plot (Suggestions Needed) by jkim ▴ 170
How much variance were explained by PC1 and PC2? It doesn't look like that the largest source of variation came from the genotype differenc…
Comment: How to trim transcripts using information from NCBI contamination screen report by Lada ▴ 30
Thank you and yes, I agree going step back is the best option but I am in a hurry at the moment so I just need to stick to the transcriptom…
Comment: How to convert plink files to Hapmap Format by Sofia • 0
Thank you so much for helping me out! I did the steps you mentioned but still got the same issue as shown in the snapshot ![enter image des…
Comment: different FeatureCounts output for the same data by Istvan Albert 100k
Make sure you are using the same version of featureCounts, it has changed how it deals with paired end reads. The exact same command will p…
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