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1,058 results • Page 3 of 22
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0
votes
3
replies
3.2k
views
Batch correction (mass spectrometry data)
Combat R SVA Biostatistics batch-effect
updated 15 days ago by 43k • written 7.5 years ago by • 0
0
votes
1
reply
3.2k
views
Removing batch effects from RPKM data
limma removeBatchEffect batch-effect rpkm
updated 16 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 15 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 16 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 15 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 15 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 24 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 15 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 16 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 15 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 15 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 14 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 16 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 17 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 17 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 18 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 15 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 16 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 16 days ago by 43k • written 5.9 years ago by ▴ 520
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma gwas
updated 4 days ago by • 0 • written 4.9 years ago by ▴ 90
0
votes
1
reply
2.8k
views
Can't make sva comparison despite very distinct batch effects
sva batch-effect
updated 16 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 17 days ago by 43k • written 2.0 years ago by ▴ 60
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 9 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 24 days ago by 43k • written 6.5 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 16 days ago by 43k • written 6.3 years ago by ▴ 40
2
votes
5
replies
2.7k
views
primer design to discriminate sequences in intron-exon MSA
primer MSA intron-exon
updated 28 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 24 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 16 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 24 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 15 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 16 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 16 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 4 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 16 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 15 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 4 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 25 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 11 days ago by 10k • written 6.2 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 17 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 16 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 8 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 25 days ago by 43k • written 3.7 years ago by ▴ 20
3
votes
3
replies
2.4k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 8 days ago by • 0 • written 22 months ago by ▴ 180
1
vote
5
replies
2.4k
views
Shannon vs Simpson for TCR diversity estimation
TCR shannon simpson
updated 22 days ago by 82k • written 5.1 years ago by ▴ 750
12
votes
4
replies
2.3k
views
long read + salmon? (transcript abundance)
long-read salmon
updated 28 days ago by 43k • written 14 months ago by ▴ 50
1
vote
14
replies
2.3k
views
Extract gRNA sequence using cutadapt
cutadapt trimming crispr sequencing
updated 1 day ago by 142k • written 4.5 years ago by ▴ 20
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma microarray differential-gene-expression
updated 24 days ago by 43k • written 6.1 years ago by ▴ 170
2
votes
5
replies
2.3k
views
DGE on transcriptomic data, focus on transcript sequences or in derivated ORFs?
differential-gene-expression RNA-Seq ORFs
updated 24 days ago by 43k • written 6.5 years ago by ▴ 90
1,058 results • Page 3 of 22
Recent Votes
Merging a large number of VCF files
A: Merging a large number of VCF files
A: pulling snps from vcf file using ids
pulling snps from vcf file using ids
Comment: No INFO/info value in headers
how to combine multiple RNAseq count files into a single dataframe in R and unix
Comment: Greatly speed up conda by using mamba
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Recent Replies
Answer: The GDC Legacy Archive is retiring soon. by lcordeiro ▴ 40
Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome by chrchang523 10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file? by chrchang523 10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
Answer: visualize GSEA by bk11 ★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R by swbarnes2 14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R by Erina • 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read by swbarnes2 14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix by Mbofire • 0
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Comment: Easy way to find out which allele is minor allele from bed file? by curious ▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file by GenoMax 142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme by e.r.zakiev ▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ by Maverick ▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ by GenoMax 142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ by Maverick ▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R by swbarnes2 14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
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