Limit : this month
all time today this week this month this year
1,076 results • Page 3 of 22
Sort: Views
Rank Views Votes Replies
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 11 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 17 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 18 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 9 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 9 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 11 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 10 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 9 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 9 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 18 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 9 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 10 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 9 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 9 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 11 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 11 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 9 days ago by 6.4k • written 15 months ago by ▴ 130
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq breast cancer subtyping
updated 11 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 12 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 9 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 10 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 11 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 10 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 11 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 18 days ago by 43k • written 6.4 years ago by ▴ 10
0
votes
4
replies
2.7k
views
Lositan freezing when generating selection table
LOSITAN
updated 3 days ago by • 0 • written 8.3 years ago by • 0
2
votes
5
replies
2.7k
views
primer design to discriminate sequences in intron-exon MSA
primer MSA intron-exon
updated 22 days ago by • 0 • written 6.6 years ago by ▴ 630
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 11 days ago by 43k • written 2.0 years ago by ▴ 60
3
votes
16
replies
2.7k
views
design matrix for dge
limma differential-gene-expression r
updated 18 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 11 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 18 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 9 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 10 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 11 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 10 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 9 days ago by 43k • written 7.0 years ago by ▴ 80
2
votes
3
replies
2.5k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel gatk calling snp variant
updated 14 hours ago by • 0 • written 23 months ago by ▴ 120
8
votes
6
replies
2.5k
views
Batch effect removal with the help of sva
SVA batch-effect gene-expression
updated 20 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 5 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 10 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 11 days ago by 43k • written 21 months ago by ▴ 20
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 3 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 20 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 17 days ago by 82k • written 5.1 years ago by ▴ 750
3
votes
3
replies
2.3k
views
How to make a TSS enrichment plot in ATAC-seq analysis?
ATAC
updated 3 days ago by • 0 • written 22 months ago by ▴ 180
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma microarray differential-gene-expression
updated 18 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 18 days ago by 43k • written 6.4 years ago by ▴ 90
12
votes
4
replies
2.3k
views
long read + salmon? (transcript abundance)
long-read salmon
updated 23 days ago by 43k • written 14 months ago by ▴ 50
1,076 results • Page 3 of 22
Recent Votes
How to input margin to UpsetR figure
Comment: How to assign cell types after integration in scRNA
NGS forensics: how to know if data is fabricated
Answer: ChIP-seq datasets: input samples omitted?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
A: Deeptools plotHeatmap - Maintain Order of Input BED file
Comment: NGS forensics: how to know if data is fabricated
Recent Locations • All
United Kingdom, just now
Israel, 1 minute ago
United States, 6 minutes ago
South Korea, 10 minutes ago
Bologna, 11 minutes ago
United Kingdom, 12 minutes ago
European Union, 14 minutes ago
Recent Awards • All
Popular Question to husensofteng ▴ 410
Popular Question to Raheleh ▴ 260
Popular Question to Aspire ▴ 300
Popular Question to rene.j.erhardt ▴ 20
Popular Question to yueli7 ▴ 250
Teacher to Wayne ★ 2.0k
Popular Question to a_bis ▴ 40
Recent Replies
Comment: Downloading full alignments from Pfam by GenoMax 141k
Not as convenient but the entire set of full alignments can be downloaded here: https://ftp.ebi.ac.uk/pub/databases/Pfam/current_release/Pf…
Comment: How many reads for WGS Sequencing? by GenoMax 141k
> What does clipped Fastq mean? Probably means that NCBI has already scanned and trimmed adapter sequencers. > both forward and revers…
Comment: How many reads for WGS Sequencing? by GenoMax 141k
You can use the default `adapters.fa` file included in the `resources` folder of [**BBMap suite**][1] (program to use is `bbduk.sh`) or a p…
Comment: How many reads for WGS Sequencing? by GenoMax 141k
Only way to find out is to try. It may work but if it is not going to then you will find that out quick (process would likely crash because…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Also, there is no mention of adapter sequence so which adapter sequence should i use to remove it from some other reads?
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Also, Do you think i can reproduce at least most part of the data from the paper just on my laptop? It has 4 logical processors (Intel(R) C…
Comment: NGS forensics: how to know if data is fabricated by Philipp Bayer 8.3k
While I think this is an interesting case, I've before found cleaned 'raw' data on SRA. It happens: bioinformaticians receive the raw data,…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
1. What does clipped Fastq mean? both forward and reverse reads in the same file? 2. Why would you remove 2000bp contigs? I feel it will gi…
Comment: How many reads for WGS Sequencing? by Ruqaiya • 0
Well, I downloaded both the reads from-[LINK][1]. Thats all i did. Thats the only thing i need to do, right? I'l try spades. [1]: http…
Comment: How to assign cell types after integration in scRNA by Francesco ▴ 10
Thanks for the fast reply.. however i had only partially understood the answer. Is correct saying that low-representation integration and b…
Answer: Can I run cellassign on samples independently if there is batch effect present? by Francesco ▴ 10
Hi! Whenever you do make independent analysis or aggregate data and analyze them, most cell type assignment tools start from raw counts to …
Comment: gvcf joint calling by zihanss • 0
Thanks for your comment, I get it now.
Answer: ChIP-seq datasets: input samples omitted? by ATpoint 82k
In my hands (and from what I know based on many years here) inputs are almost exclusively used during peak calling to correct for loci-spec…
Comment: How to assign cell types after integration in scRNA by ATpoint 82k
No difference here. After all you typically want a label per cluster/group, so either subset to the control condition to do the assignment,…
Comment: Differential Expression using Isoseq-supplemented reference transcriptome by gaoanwei • 0
I found the question and ASK the GPT4 turbo
Traffic: 1934 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6