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1,000 results • Page 3 of 20
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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 6 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 7 days ago by 43k • written 7.0 years ago by ▴ 20
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 8 days ago by 43k • written 7.4 years ago by • 0
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq countOverlaps R
updated 8 days ago by 43k • written 6.3 years ago by ★ 1.9k
1
vote
3
replies
3.4k
views
How to correct for batch effect in microarray meta-analysis
ComBat microarray meta-analysis batch-effect
updated 6 days ago by 43k • written 9.9 years ago by ▴ 120
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 8 days ago by 43k • written 5.2 years ago by ▴ 120
3
votes
4
replies
3.3k
views
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
next-gen
updated 14 days ago by 43k • written 6.7 years ago by ▴ 10
1
vote
8
replies
3.3k
views
cutadapt error problem
next-gen cutadapt
updated 27 days ago by 43k • written 5.6 years ago by ▴ 20
1
vote
3
replies
3.3k
views
How to calculate Differential Gene expression between samples with replicates
Differential-Gene-Expression RNA-Seq
updated 15 days ago by 43k • written 7.8 years ago by • 0
0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat R SVA Biostatistics batch-effect
updated 6 days ago by 43k • written 7.4 years ago by • 0
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq batch-effect
updated 6 days ago by 43k • written 7.1 years ago by ▴ 40
0
votes
1
reply
3.1k
views
Removing batch effects from RPKM data
limma removeBatchEffect batch-effect rpkm
updated 8 days ago by 43k • written 8.5 years ago by ▴ 360
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 7 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 6 days ago by 43k • written 9.0 years ago by • 0
0
votes
3
replies
3.0k
views
Is there any method for using WES data from Illumina Hiseq into ABSOLUTE?
R next-gen-sequencing absolute
updated 27 days ago by 43k • written 6.7 years ago by • 0
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq batch-effect sequencing
updated 6 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 15 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 6 days ago by 43k • written 7.9 years ago by ★ 3.4k
0
votes
2
replies
2.9k
views
Should I pre-normalize RNAseq data before combat?
RNA-Seq combat batch-effect R
updated 7 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 6 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 6 days ago by 43k • written 6.6 years ago by ▴ 100
0
votes
0
replies
2.8k
views
TCGA RNAseqVer2 batch effects
TCGA RNA-Seq batch-effect
updated 8 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 8 days ago by 43k • written 7.9 years ago by ▴ 50
7
votes
3
replies
2.8k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 6 days ago by 6.4k • written 15 months ago by ▴ 130
1
vote
5
replies
2.8k
views
Batch effect identification using PCA
PCA qRT-PCR R targeted-assay Batch-Effect
updated 9 days ago by 43k • written 3.9 years ago by ▴ 250
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq breast cancer subtyping
updated 8 days ago by ▴ 70 • written 5.7 years ago by ▴ 50
0
votes
2
replies
2.8k
views
RNA-seq unbalanced batch effect correction
limma RNA-Seq edgeR batch-effect
updated 6 days ago by 43k • written 7.0 years ago by • 0
1
vote
1
reply
2.8k
views
removing batch effects from large number of data sets
Microarray batch-effect
updated 8 days ago by 43k • written 5.9 years ago by ▴ 520
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq RNA-Seq batch-effect DESeq2
updated 7 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 7 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 8 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
2
votes
5
replies
2.7k
views
primer design to discriminate sequences in intron-exon MSA
primer MSA intron-exon
updated 19 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 15 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 8 days ago by 43k • written 9.9 years ago by ★ 2.7k
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 8 days ago by 43k • written 2.0 years ago by ▴ 60
4
votes
9
replies
2.6k
views
Tool: CANEapp, a user-friendly application for automated next generation transcriptomic data analysis
RNA-Seq
written 8.2 years ago by • 0
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
4
replies
2.6k
views
Lositan freezing when generating selection table
LOSITAN
updated 13 hours ago by • 0 • written 8.3 years ago by • 0
5
votes
2
replies
2.6k
views
How do you evaluate the effectiveness of the batch effect algorithm?
Batch-Effect
updated 6 days ago by 43k • written 9.1 years ago by ▴ 110
4
votes
4
replies
2.6k
views
Advice on Handling Batch Effect in ChIP-seq Experiment
ChIP-Seq batch-effect sequencing
updated 7 days ago by 43k • written 4.6 years ago by ▴ 20
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 8 days ago by 43k • written 6.7 years ago by • 0
8
votes
6
replies
2.6k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 7 days ago by 3.0k • written 24 months ago by ▴ 230
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 6 days ago by 43k • written 7.0 years ago by ▴ 80
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA batch-effect gene-expression
updated 16 days ago by 43k • written 3.5 years ago by ▴ 240
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink PED
updated 2 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
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect omniexpress GWAS GSA
updated 7 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 8 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
1,000 results • Page 3 of 20
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What is the difference between HaplotypeCaller and UnifiedGenotyper?
What is the difference between HaplotypeCaller and UnifiedGenotyper?
RSeQC Output from infer_experiment.py - what does it mean?
ScRNAseq-How to correctly choose cell type marker genes
ScRNA data question
Comment: SRA to BAM
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Recent Replies
Comment: GAPIT p-value significance threshold by ginellegrenier • 0
Hi, I was wondering if you have found a solution to this? Thanks!
Comment: PCA plot by jkim ▴ 170
cross posted in bioconductor. [https://support.bioconductor.org/p/9157968/][1] [1]: https://support.bioconductor.org/p/9157968/
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Which normalization method did you use for your data? I am guessing you had used SCTransform normalization for your data. Can you plot usin…
Comment: How to make a TSS enrichment plot in ATAC-seq analysis? by sp • 0
Hi Dan, I was wondering if you found out how to make the same graph with NFR and NBR regions with different curves. I was able to recreate…
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I think the coverage could also computed from bam file itself, but let say I do not include the coverage, do you have any idea why it needs…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas by GenoMax 141k
I am moving my answer to a comment. At this point you should email NCBI help desk and ask them this question. If you get an answer then ple…
Comment: Figures are disappeared from html report of SnpEff by Pierre Lindenbaum 161k
the javascript in your html is deprecated or your firefox is just tool old.
Comment: Why gatk VariantAnnotator required bam and coverage files by Pierre Lindenbaum 161k
> I would like to ask why they may require the bam file for this function? hum.. if you want to add the coverage, where do you think gatk …
Comment: Figures are disappeared from html report of SnpEff by analyst ▴ 30
By following above approach I got this ![enter image description here][1] [1]: /media/images/b47490eb-d4c4-4f39-a7b2-f5b7b6b8
Comment: Highest variable features in single cell data by Kazo • 0
I apologize for the confusion. What I meant to say is that, for example, the Trbv17 gene appears among the variable genes. However, when I …
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I manage to find a workwround, but I don't understand what I did wrong here. my solution was to extract the cluster column as vector and…
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Hi, thanks for letting us know. In a recent software update, we introduced a problem with the written splice information in the cached …
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so which one should i prefer? i don't need the entire results i need the condition-Germline table only. (for eg:-from, https://www.ncbi.nlm…
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OK, not sure why your intention is to use RSEM p-values for, but at least tell us the commands you ran then otherwise how are we supposed t…
Comment: Fetch table from clinvar database according to a list of rsid by Pierre Lindenbaum 161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
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