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975 results • Page 6 of 20
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1
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4
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397
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Limma Analysis Agilent Microarray Data (GPL1708)
Microarray Limma Agilent
7 days ago by hagl ▴ 10
2
votes
4
replies
364
views
Should I use unpaired reads from trimmomatic
RNA-seq QC Trimmomatic
updated 13 days ago by 14k • written 14 days ago by • 0
2
votes
4
replies
6.1k
views
Batch Effect Removal in RNA-Seq Data for DGE & WGCNA. Should I omit any samples according to PCA plots?
Batch-effect RNA-Seq R DESeq2
updated 18 days ago by 43k • written 7.6 years ago by ▴ 70
2
votes
4
replies
424
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 26 days ago by 142k • written 27 days ago by • 0
5
votes
4
replies
378
views
Forum: Ideal PC configurations and operating system for bioinformatics laboratory
PC
4 days ago by Estevão • 0
1
vote
4
replies
734
views
What happened to Tombo Re-squiggle
Tombo resquiggle ONT
updated 18 days ago by 43k • written 3 months ago by • 0
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq batch-effect Random-Forest
updated 19 days ago by 43k • written 4.7 years ago by ▴ 10
0
votes
4
replies
2.0k
views
Requesting help with RNA-Seq differential gene analysis
differential-gene-expression deseq2
updated 27 days ago by 43k • written 6.2 years ago by ▴ 50
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 19 days ago by • 0 • written 4.6 years ago by ▴ 40
1
vote
4
replies
453
views
Is it just me or has www.ensembl.org been broken for a while?
ensembl
25 days ago by gene_biostars • 0
4
votes
4
replies
353
views
How to fetch published paper of a BioProject
BioProject pumbed NGS
27 days ago by Morteza • 0
4
votes
4
replies
392
views
Bowtie2 mapping is slow
metagenomics bowtie2 mapping read
updated 24 days ago by 6.4k • written 4 weeks ago by • 0
9
votes
4
replies
2.0k
views
Integration of RNA-Seq data with microarray data
microarray RNA-Seq batch-effect R
updated 19 days ago by 43k • written 4.0 years ago by ▴ 30
3
votes
4
replies
3.3k
views
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
next-gen
updated 25 days ago by 43k • written 6.7 years ago by ▴ 10
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq breast cancer subtyping
updated 19 days ago by ▴ 70 • written 5.7 years ago by ▴ 50
3
votes
4
replies
717
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
14 days ago by rahu • 0
2
votes
4
replies
355
views
SnpEff annotates coding duplication as intronic?
snpeff
19 days ago by kirill.zaslavsky • 0
2
votes
4
replies
411
views
Which command ro run MAKER pipeline for gene annotation ?
run. command to MAKERpipeline.
updated 21 days ago by 142k • written 22 days ago by ▴ 10
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect transcriptomics
updated 18 days ago by 43k • written 2.6 years ago by ▴ 30
0
votes
4
replies
442
views
Gene Ontology question
differential-expression Gene-ontology
updated 27 days ago by 43k • written 5 weeks ago by • 0
1
vote
4
replies
3.2k
views
remove batch effect for multiple tumor data
RNA-Seq batch-effect
updated 18 days ago by 43k • written 7.1 years ago by ▴ 40
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R RNA-Seq combat python batch-effect
updated 18 days ago by 43k • written 7.1 years ago by ▴ 310
0
votes
4
replies
263
views
Genbank File Format
gbkformat
6 days ago by alenew.am • 0
2
votes
4
replies
376
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
12 days ago by HyperEvo • 0
1
vote
4
replies
1.3k
views
Comparing RNA-Seq data to online databases
RNA-Seq batch-effect
updated 19 days ago by 43k • written 4.7 years ago by ▴ 10
4
votes
4
replies
445
views
How do I install plink2 on a mac?
plink2 plink
updated 21 days ago by 11k • written 24 days ago by ▴ 10
0
votes
4
replies
830
views
Differential gene expression
limma differential-gene-expression R
updated 27 days ago by 43k • written 4.0 years ago by ▴ 40
5
votes
4
replies
690
views
DEG analysis of RNA-seq data across multiple tissues and two conditions
RNA-seq EdgeR DEGs DESeq2
18 days ago by BioinfGuru ★ 1.7k
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq RNA-Seq batch-effect DESeq2
updated 19 days ago by 43k • written 5.1 years ago by ★ 2.6k
0
votes
4
replies
275
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq GO
updated 6 days ago by 43k • written 7 days ago by ▴ 50
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression RNA-Seq DESeq2
updated 27 days ago by 43k • written 8.1 years ago by ▴ 80
8
votes
4
replies
3.0k
views
Read count correlation between samples
differential-gene-expression RNA-seq
updated 27 days ago by 43k • written 6.5 years ago by ★ 1.6k
0
votes
4
replies
292
views
Question regarding WGCNA
WGCNA Network-construction
updated 5 hours ago by 3.6k • written 3 days ago by • 0
0
votes
4
replies
358
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 25 days ago by 142k • written 27 days ago by • 0
3
votes
4
replies
403
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI. cDNA
updated 23 days ago by 161k • written 23 days 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 11 days ago by • 0 • written 2.5 years ago by • 0
1
vote
4
replies
389
views
Homer giving troubles
homer HOMER
28 days ago by naveedhasan2000 • 0
1
vote
4
replies
835
views
I want to calculate if the sample has whole genome duplication event or not?
sequencing wgs
27 days ago by Hyper_Odin ▴ 310
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray combat batch-effect median-normalization
updated 18 days ago by 43k • written 18 months ago by • 0
0
votes
4
replies
581
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq gene-expression
updated 16 days ago by 82k • written 17 days ago by ▴ 140
5
votes
4
replies
362
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger scRNA-seq 10x
20 days ago by Spring • 0
0
votes
4
replies
629
views
Per base sequence content failed miserably
fastqc sequence trimmomatic NGS assembly
17 days ago by Kai Xin • 0
2
votes
4
replies
2.6k
views
When to use .vcf or .gvcf files from GATK HaplotypeCaller?
indel gatk calling snp variant
updated 7 days ago by 9.7k • written 24 months ago by ▴ 120
1
vote
4
replies
317
views
Segmentation error while using a tool
smalt
updated 2 days ago by ★ 27k • written 2 days ago by • 0
3
votes
4
replies
389
views
Why gatk VariantAnnotator required bam and coverage files
gatk VariantAnnotator
11 days ago by QX • 0
2
votes
4
replies
1.2k
views
PLINK p value returning NA
GWAS PLINK
updated 28 days ago by 10k • written 19 months ago by • 0
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq batch-effect deseq
updated 18 days ago by 43k • written 2.3 years ago by • 0
1
vote
4
replies
458
views
Database or Tool: Identifying Gene Regions (Exon/Intron/UTR) from Chromosome Position
gene-region biomart ucsc-browser intron exon
updated 27 days ago by 142k • written 27 days ago by • 0
3
votes
4
replies
3.8k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect microarray R
updated 19 days ago by 43k • written 2.9 years ago by ▴ 60
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect omniexpress GWAS GSA
updated 19 days ago by 43k • written 4.8 years ago by ▴ 10
975 results • Page 6 of 20
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Comment: Which hg38 file?
Answer: Which hg38 file?
Answer: Where to get the following bed file?
How to save GRanges object to csv file
Answer: How to get proteins from GFF file resulted from MAKER annotation
Answer: Gene ontology and homologs
Comment: anRichment is missing
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Recent Replies
Comment: Where to get the following bed file? by GenoMax 142k
SeqCap kits are discontinued. If you don't find the said file your will need to email Roche Support per this page: https://sequencing.roche…
Answer: Where to get the following bed file? by LChart 3.9k
UCSC maintains a list of exome probe sets and targets. You could check there: https://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/
Comment: How to compute TPM normalized values for TCGA miRNA data? by Ngrin • 0
Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 390
It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
Comment: Problem with Seurat package in PercentageFeatureSet function by bk11 ★ 2.4k
Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
Answer: How to compute TPM normalized values for TCGA miRNA data? by dsull ★ 6.0k
TPM is irrelevant for miRNA-seq; CPM works fine. TPM tries to adjust for length effects by dividing by gene length (e.g. reducing the im…
Comment: Applying the metacell2 algorithm using python by Wayne ★ 2.0k
"I'm also unsure what qualifies as a lateral gene." The [README where you reference](https://metacells.readthedocs.io/en/latest/readme.htm…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by sovrappensiero ▴ 90
Ah, yes this makes sense! I knew this was an issue with, say, using kraken2 on shotgun metagenomic reads, but I don't have a lot of experi…
Comment: How to access TCGA samples that were treated with a specific drug? by Qroid ▴ 40
Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA by Chris Dean ▴ 390
If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
Comment: anRichment is missing by GenoMax 142k
Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.
Comment: anRichment is missing by Tatyana • 0
Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(
Comment: anRichment is missing by GenoMax 142k
See this link for the WGCNA documentation and code from Peter Langfelder : https://bioinformatics.stackexchange.com/questions/21885/where-t…
Comment: anRichment is missing by Tatyana • 0
The problem is back, Horwath's lab web is down again. Is it possible to get anRichment istallation file somewhere? (The greater problem is …
Comment: 16S rRNA microbiome differential abundance analysis with DESeq2 finds same micro by andres.firrincieli 3.6k
1. Maribaculaceae is a family not a genus 2. Who said that ASV with the same taxonomic classification must have the same behaviour? 3. With…
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