Limit : this month
all time today this week this month this year
1,000 results • Page 4 of 20
Sort: Views
Rank Views Votes Replies
6
votes
10
replies
2.3k
views
Why different DEGs between my result and the author's result?
limma microarray differential-gene-expression
updated 22 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 22 days ago by 43k • written 6.5 years ago by ▴ 90
2
votes
1
reply
2.3k
views
TCGA RNAseqV2 data matrix batch effect control and remove
RNA-Seq batch-effect
updated 13 days ago by 43k • written 7.7 years ago by ▴ 10
2
votes
4
replies
2.3k
views
Negative values after batch correction using removeBatchEffect from Limma
batch limma removeBatchEffect rna-seq batch-effect
updated 15 days ago by 43k • written 21 months ago by ▴ 20
9
votes
5
replies
2.3k
views
Millions of Reads Needed for Differential Gene Expression
differential-gene-expression RNA-Seq deseq2
updated 22 days ago by 43k • written 4.6 years ago by ▴ 20
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 15 days ago by • 0 • written 4.6 years ago by ▴ 40
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq batch-effect Random-Forest
updated 14 days ago by 43k • written 4.7 years ago by ▴ 10
5
votes
4
replies
2.2k
views
How do we process Kallisto output (continuous real values) for DESEQ2 analysis (which strictly require discrete count values)?
read-counts DESEQ2 differential-gene-expression kallisto
updated 22 days ago by 43k • written 2.7 years ago by ▴ 170
4
votes
3
replies
2.2k
views
The result of differential gene expression analysis should be extracted based on adj.p.value ?
limma microarray bioconductor R
updated 15 days ago by 43k • written 6.3 years ago by ▴ 260
2
votes
5
replies
2.2k
views
Generating a heatmap in DEG analysis
Differential-gene-expression RNA-Seq
updated 22 days ago by 43k • written 3.1 years ago by ▴ 10
3
votes
1
reply
2.2k
views
Maximum Number of Gene in a DESeq2 and edgeR
Differential-Gene-Expression EdgeR DESeq2
updated 22 days ago by 43k • written 8.1 years ago by ▴ 10
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq tophat batch-effect cufflinks
updated 14 days ago by 43k • written 5.3 years ago by • 0
2
votes
2
replies
2.1k
views
How to use pacbio reads to join contigs
assembly tgs pacbio
updated 26 days ago by 43k • written 6.0 years ago by ▴ 20
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 14 days ago by 43k • written 4.8 years ago by ▴ 20
6
votes
8
replies
2.1k
views
Simple explanation and usage of WGCNA package?
wgcna RNA-Seq ChIP-Seq
updated 24 days ago by • 0 • written 3.9 years ago by ▴ 120
1
vote
0
replies
2.1k
views
Tool: DASC -- detecting hidden batch effects in gene expression datasets (Array/RNA-Seq/scRNA-Seq)
RNA-Seq scRNA-Seq R Batch-Effect
updated 13 days ago by 43k • written 6.9 years ago by ★ 1.1k
2
votes
3
replies
2.1k
views
Why the PCA results of PCASamples() from methylkit is different from prcomp()?
methylkit prcomp pca PCASamples multiplePCA
updated 25 days ago by ★ 1.2k • written 4.2 years ago by ▴ 250
1
vote
2
replies
2.1k
views
RNA-seq unbalanced batch effect correction
RNA-Seq edgeR R Batch-Effect
updated 14 days ago by 43k • written 5.7 years ago by ▴ 730
3
votes
2
replies
2.1k
views
Batch effect correction - miRNA sequencing - DESeq2
Batch-effect DESeq2 miRNA-Seq
updated 15 days ago by 43k • written 5.5 years ago by • 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference 38build impute imputation
2 days ago by anna ▴ 20
3
votes
5
replies
2.1k
views
DE analysis with edgeR and possibly batch effect
analysis edgeR batch-effect DE
updated 14 days ago by 43k • written 5.1 years ago by ★ 1.9k
0
votes
0
replies
2.1k
views
betweenLaneNormalization and calcNormFactors in RUVs
Differential-Gene-Expression RUVs RNA-Seq R
updated 22 days ago by 43k • written 6.9 years ago by ▴ 10
1
vote
6
replies
2.1k
views
DGE on protein-coding and lncRNAs separately?
differential-gene-expression RNA-seq
updated 22 days ago by 43k • written 6.5 years ago by ★ 1.6k
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation RNA-Seq R
updated 15 days ago by 43k • written 6.1 years ago by ▴ 120
0
votes
5
replies
2.1k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq batch-effect normalization
updated 15 days ago by 43k • written 21 months ago by ▴ 60
1
vote
3
replies
2.0k
views
gene expression data analysis and batch effect methods
microarray Gene-expression batch-effect
updated 13 days ago by 43k • written 6.9 years ago by ▴ 220
0
votes
0
replies
2.0k
views
NOISeq Batch Correction to RNA-seq data
Batch-effect RNA-Seq ARSyNseq limma NOISeq
updated 13 days ago by 43k • written 6.9 years ago by • 0
4
votes
6
replies
2.0k
views
RNA-Seq DGE: Evaluate model quality
differential-gene-expression RNA-Seq deseq2
updated 22 days ago by 43k • written 6.2 years ago by ★ 1.6k
0
votes
1
reply
2.0k
views
Is it appropriate to apply RUVseq on output from kallisto?
RNA-Seq batch-correction kallisto
updated 15 days ago by 43k • written 5.3 years ago by ▴ 60
0
votes
4
replies
2.0k
views
Requesting help with RNA-Seq differential gene analysis
differential-gene-expression deseq2
updated 22 days ago by 43k • written 6.2 years ago by ▴ 50
0
votes
0
replies
2.0k
views
Job: Bioinformatics Research Postdoc
RNA-Seq genome
updated 21 days ago by 43k • written 8.2 years ago by • 0
3
votes
6
replies
2.0k
views
7 follow
DNA methylation preprocessing
SWAN DNA methylation Funnorm
updated 5 days ago by 43k • written 2.4 years ago by ▴ 10
0
votes
0
replies
1.9k
views
Correcting batch effect from known variables in RnBeads using Combat
Combat 450k methylation RnBeads batch-effect
updated 13 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 13 days ago by 43k • written 7.5 years ago by ▴ 50
9
votes
4
replies
1.9k
views
Integration of RNA-Seq data with microarray data
microarray RNA-Seq batch-effect R
updated 15 days ago by 43k • written 4.0 years ago by ▴ 30
6
votes
10
replies
1.9k
views
A guide to modern genome assembly
long-reads illumina genome-assembly
updated 26 days ago by 43k • written 2.6 years ago by ★ 1.9k
4
votes
5
replies
1.9k
views
which package should be selected for differential gene expression analysis
Differential-gene-expression RNA-Seq
updated 22 days ago by 43k • written 5.5 years ago by ▴ 100
2
votes
5
replies
1.9k
views
Differential Expression Analysis with batches which have different biological groups
R RNA-Seq limma DE batch-effect
updated 14 days ago by 43k • written 4.8 years ago by ▴ 60
1
vote
2
replies
1.9k
views
Remove batch effect from exome data
NGS exome-sequencing batch-effect
updated 13 days ago by 43k • written 6.6 years ago by ▴ 270
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression TPM RNA-Seq counts batch-effect
14 days ago by Ram 43k
0
votes
7
replies
1.9k
views
Batch effect correction in RNASeq data and plot Dendrograms cluster
clustering dendrogram RNA-Seq batch-effect
updated 13 days ago by 43k • written 4.0 years ago by ▴ 500
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 15 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 15 days ago by 43k • written 3.5 years ago by ▴ 50
38
votes
24
replies
1.8k
views
10 follow
NGS forensics: how to know if data is fabricated
fastq STAR NGS Illumina
updated 2 days ago by 19k • written 4 days ago by ▴ 580
2
votes
2
replies
1.8k
views
Time point microarray data correcting for batch effects
microarray combat batch-effect
updated 13 days ago by 43k • written 6.7 years ago by ▴ 10
0
votes
3
replies
1.8k
views
How to remove batch effect in copy number segment mean
Combat CNA Batch-Effect
updated 14 days ago by 43k • written 5.5 years ago by ▴ 150
4
votes
2
replies
1.8k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF SAM BAM GFF minimap2
updated 15 days ago by ▴ 130 • written 12 months ago by • 0
0
votes
5
replies
1.8k
views
Demultiplexing multiple amplicons from one fastq based on primer sequence
demultiplexing illumina
updated 23 days ago by 3.2k • written 3.4 years ago by • 0
1
vote
2
replies
1.8k
views
Data processing order: normalisation or batch effect correction first?
limma proteome batch-effect R
updated 15 days ago by 43k • written 3.5 years ago by ▴ 340
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 13 days ago by 43k • written 6.7 years ago by ▴ 80
1,000 results • Page 4 of 20
Recent Votes
Answer: Problem with data downloaded from Short Reads Archive (SRA)
Answer: Super ehancers
Comment: Bacterial plasmid analysis
Answer: Why employ normalization methods, and how can they be utilized in DEG analysis?
Answer: Why employ normalization methods, and how can they be utilized in DEG analysis?
Answer: What analysis suitable to identify similarly expressed genes between two samples
Comment: Bacterial plasmid analysis
Recent Locations • All
Italy, just now
Indiana University, just now
United Kingdom, just now
United States, 1 minute ago
Russia, 2 minutes ago
United States, 3 minutes ago
United Kingdom, 3 minutes ago
Recent Awards • All
Popular Question to hafiz.talhamalik ▴ 350
Popular Question to Hayler Edu ▴ 40
Popular Question to eesiribloom ▴ 80
Popular Question to g.persic1991 • 0
Popular Question to massa.kassa.sc3na ▴ 600
Teacher to shenwei356 8.5k
Popular Question to Apex92 ▴ 280
Recent Replies
Comment: Do I need to go back and filter my long-reads? by Ram 43k
Do not delete posts that have received feedback. Engage with the user providing you feedback.
Answer: Download eQTL data of one specific gene for all tissues from GTEx by bk11 ★ 2.4k
Please kindly check your result here. You can click `csv` and download the date in this [link][1]. **OR** If you prefer to use R, there i…
Comment: RNAseq one control two conditions, shared and exclusive genes by matteo.levorato • 0
but why not a single matrix with the 3 different condition and then by lfcShrink function get the DEGs of each condition?
Answer: Super ehancers by jared.andrews07 ★ 16k
Sure, you can run it on them. Stitching tends to happen less frequently since the ATAC peaks are generally less wide than H3K27ac, but it'l…
Answer: What purposes can TPM values be used for? by jared.andrews07 ★ 16k
TPMs cannot be used for intersample comparisons, but they can be used for intrasample comparisons (e.g. comparing relative expression level…
Comment: Bacterial plasmid analysis by nicole.kavanagh • 0
Thank you so much for the recommendation and the very clear explanation , it's much appreciated. I have already made core-gene phylogenies/…
Comment: What purposes can TPM values be used for? by Adam ▴ 30
Have you run FASTQC and checked the mapping efficiency of WT3? > would running DESeq using TPM values help solve my problem? No, DESeq sh…
Answer: How goes gene length effect the number of reads mapped by i.sudbery 19k
See my answer about the what hows and whens of RNA-seq normalisation here: https://www.biostars.org/p/9586553/#9586566
Comment: What purposes can TPM values be used for? by dsull ★ 5.9k
Since you have mutant vs wild-type, using DESeq2 is the right thing to do. Rather than showing a small table of numbers, you should make a …
Answer: What purposes can TPM values be used for? by i.sudbery 19k
See my post here for more details on RNA-seq normalisation: https://www.biostars.org/p/9586553/#9586566 In short, TPM normalises for ge…
Comment: Bacterial plasmid analysis by Zamin Iqbal ▴ 10
I vote for this, it's the best! (but also, I am Daria's PhD supervisor so I am biased). Preprint out soon(ish) [no pressure Daria!]
Comment: Downsampling long-read BAM files by GenoMax 142k
Is this what you used ultimately? Did this tool satisfy the "specific average depth" requirement? You could accept (green check mark) this…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory by Estevão • 0
Thank you. My budget is around 20 thousand dollars.
Answer: Problem with data downloaded from Short Reads Archive (SRA) by atharvakarkare14 ▴ 30
Prefetch files using sratoolkit **prefetch** command and then use **fasterq-dump**. There you can see the number of reads. For validation, …
Answer: Downsampling long-read BAM files by eesiribloom ▴ 80
random downsampling of bam files is now possible using [rasusa][1] [v1.0.0][2] with the `aln` subcommand [1]: https://github.com/mbh…
Traffic: 3076 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