Limit : this year
all time today this week this month this year
1,000 results • Page 1 of 20
Sort: Votes
Rank Views Votes Replies
20
votes
17
replies
3.3k
views
How to add "transcript" feature to a gtf file?
gtf
updated 10 months ago by ★ 1.2k • written 3.3 years ago by ▴ 110
15
votes
16
replies
1.8k
views
ncbi error report log for validate fastq issue
sra-tools
updated 7 months ago by 142k • written 7 months ago by ★ 1.2k
14
votes
10
replies
957
views
How to remove center population from seurat cluster
single-cell
4 months ago by synat.keam ▴ 100
14
votes
18
replies
2.3k
views
Clustering in single cell
seurat single-cell
updated 6 months ago by ▴ 210 • written 7 months ago by ▴ 260
13
votes
22
replies
11k
views
SVA : Setting up the data from an ExpressionSet and applying sva function to extimate batches
sva combat batch-effect
updated 19 days ago by 43k • written 6.8 years ago by ★ 1.3k
11
votes
22
replies
4.2k
views
No significant DEG: A request to double check my commands for limma.
limma differential-gene-expression
updated 27 days ago by 43k • written 5.0 years ago by ▴ 270
10
votes
6
replies
984
views
RNA seq, secreted protein
protein gene secreted
updated 9 months ago by 21k • written 17 months ago by ▴ 170
10
votes
15
replies
1.8k
views
Can't find a variant which suppose must have in a vcf file
variant-calling bcftools nf-core
10 months ago by Chris ▴ 260
10
votes
14
replies
5.0k
views
ATAC-seq data and deepTools: Small detail with impact on output
bigwig read-length deeptools ATAC-seq
updated 11 months ago by 43k • written 4.2 years ago by ▴ 50
10
votes
7
replies
3.7k
views
What is Pathway Analysis?
database analysis ontology pathway
updated 10 months ago by 43k • written 8.1 years ago by ▴ 330
9
votes
13
replies
15k
views
Sort bam file by coordinates using samtools
next-gen-sequencing gene rna-seq
updated 10 months ago by 43k • written 5.6 years ago by ▴ 30
9
votes
15
replies
1.3k
views
Construction of single sequence assembly out of contigs
Contigs Bacteria Genome WGS
5 months ago by analyst ▴ 30
9
votes
5
replies
507
views
Annotation of Complex Heatmap
complexheatmap
3 months ago by abiuma ▴ 30
9
votes
5
replies
732
views
Prophage prediction tool
prophage PHASTER prediction
updated 9 months ago by 142k • written 9 months ago by ▴ 160
8
votes
7
replies
1.1k
views
Why does Ensembl VEP provide HGVSg for some variants and not others?
vcf VEP
11 months ago by Jeremy Leipzig 22k
8
votes
5
replies
840
views
Frustrated with DEA results
microarray differential-expression
updated 7 months ago by ★ 6.0k • written 7 months ago by • 0
8
votes
5
replies
2.0k
views
BLASTp command line : filtering results by a minimum % of identity and % coverage
BLASTp
updated 7 months ago by 43k • written 2.6 years ago by ▴ 160
8
votes
10
replies
2.1k
views
PyWGCNA
WGCNA
10 months ago by yoshifumimiya ▴ 40
8
votes
10
replies
769
views
bash script
whole-genome-sequencing
updated 21 days ago by 43k • written 28 days ago by ▴ 30
8
votes
6
replies
939
views
How to create a Venn Diagram for overlapping SVs from a merged VCF
truvari structural-variants r vcf venn-diagram
6 months ago by Matteo Ungaro ▴ 100
8
votes
7
replies
584
views
adjusting parameters in ViolinPlot did not work
single-cell
updated 12 weeks ago by 43k • written 12 weeks ago by ▴ 100
7
votes
7
replies
5.0k
views
RNA-Seq time series analysis using a DESeq2 spline approach yields far too many significant genes
splines DESeq2 time-series RNA-Seq
updated 11 months ago by 43k • written 5.3 years ago by ▴ 80
7
votes
6
replies
1.4k
views
On "wings" in volcano plots...
DEG volcano DGE statistics DE
updated 11 months ago by 82k • written 11 months ago by ▴ 190
7
votes
8
replies
9.0k
views
Determining read count
trimmomatic rna-seq trinity
updated 8 months ago by 43k • written 8.0 years ago by ▴ 110
7
votes
13
replies
4.4k
views
6 follow
Is trimming necessary for RNAseq?
RNA-Seq trimming fastqc
updated 6 months ago by 82k • written 3.5 years ago by ▴ 10
7
votes
13
replies
979
views
deal with PCA and my samples
PCA DEG meta-analysis
6 months ago by ali • 0
7
votes
7
replies
1.9k
views
Sort and convert the SAM files to BAM
samtools RNA-seq NGS
updated 8 months ago by 43k • written 5.8 years ago by ▴ 40
7
votes
7
replies
608
views
6 follow
PCA plot interpretation (single population)
PCA GWAS pruning
3 months ago by Shane ▴ 20
7
votes
8
replies
4.2k
views
DEseq2 design matrix with 3 factors
RNA-seq deseq2
updated 11 months ago by 43k • written 3.9 years ago by ▴ 60
7
votes
9
replies
1.2k
views
Calculation of TMB on gene level
genomics
updated 7 months ago by ▴ 680 • written 7 months ago by ▴ 20
7
votes
3
replies
1.6k
views
What are the best tools for Genome assembly
Assembly genome
updated 10 months ago by 43k • written 5.8 years ago by ▴ 10
7
votes
12
replies
1.7k
views
How to pass arguments in a bash script to perform read alignment to the reference?
exome bwa bash
updated 6 months ago by 43k • written 4.2 years ago by ▴ 310
6
votes
3
replies
2.0k
views
Gene network with expression data
network RNA-Seq
updated 10 months ago by 43k • written 6.5 years ago by ▴ 30
6
votes
7
replies
1.8k
views
Reference genome for RNA-Seq reads decontamination
FastQ_Screen RNA-Seq
updated 8 months ago by 43k • written 4.1 years ago by ▴ 70
6
votes
5
replies
773
views
merging replicates
ChIP-seq
updated 4 months ago by 82k • written 4 months ago by • 0
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 19 days ago by 43k • written 4.7 years ago by ▴ 60
6
votes
4
replies
6.6k
views
What is gnomAD allele frequency
AF gnomAD
updated 3 months ago by ▴ 760 • written 3.1 years ago by ▴ 50
6
votes
7
replies
583
views
NF-Core ampliseq - Rscript markdown error
nf-core ampliseq
updated 3 months ago by 54k • written 3 months ago by • 0
6
votes
8
replies
1.2k
views
conda: command not found: gatk.
conda gatk
11 months ago by bestone ▴ 30
6
votes
1
reply
456
views
16S vs shotgun tools
metagenomics
9 months ago by anasjamshed ▴ 120
6
votes
5
replies
731
views
Tests for the linear and non-linear relationship between two genes
ode drc correlation regression rnaseq
updated 4 months ago by 82k • written 4 months ago by ▴ 40
6
votes
2
replies
847
views
Can the input file name be the same as the output file in `samtools sort`?
Samtools
updated 10 months ago by 43k • written 2.2 years ago by ▴ 180
6
votes
2
replies
733
views
miRNA tool for search targets for genes
mirna targets
updated 10 months ago by 43k • written 2.8 years ago by ★ 1.2k
6
votes
6
replies
3.2k
views
ChIP-Seq Intensity Analysis
R ChIP-Seq
updated 11 months ago by 43k • written 6.4 years ago by ▴ 20
6
votes
12
replies
2.0k
views
Help with error in cellranger
Cellranger
updated 11 months ago by 142k • written 11 months ago by ▴ 260
6
votes
9
replies
2.0k
views
Error when runing Bowtie2: (ERR): bowtie2-align exited with value 1
BAM Bowtie
updated 12 months ago by 43k • written 15 months ago by ▴ 50
6
votes
3
replies
567
views
Optimal Over Representation Analysis DE genes foldFC threshold?
ClusterProfiler ORA EnrichGo DGE
updated 9 months ago by 4.2k • written 9 months ago by ▴ 100
6
votes
9
replies
2.9k
views
How to analyze the scRNA seq Fastq files from NCBI
SRAtool Cellranger NCBI
updated 10 months ago by 43k • written 2.3 years ago by ▴ 20
6
votes
5
replies
707
views
Log2 transformation is well used, but is there a good paper that can be used as reference ?
TPM log2-transformation r
updated 4 months ago by 87k • written 4 months ago by ▴ 140
6
votes
3
replies
648
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics box-plot R scale_adjustment logarithm
updated 5 months ago by ▴ 910 • written 5 months ago by ▴ 40
1,000 results • Page 1 of 20
Recent Votes
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
Comment: Gene Specific coverage from WGS data
Comment: Gene Specific coverage from WGS data
Comment: High Malat-1 expression in single cell data
Recent Locations • All
United States, just now
Spain, 1 minute ago
USA, 2 minutes ago
Uruguay, 3 minutes ago
United States, 4 minutes ago
United States, 5 minutes ago
United States, 5 minutes ago
Recent Awards • All
Popular Question to Scott McKay ▴ 30
Popular Question to A. Domingues ★ 2.7k
Scholar to LChart 3.9k
Popular Question to JACKY ▴ 140
Popular Question to bhumm ▴ 140
Teacher to Matthias Zepper 4.6k
Popular Question to sidrah.maryam ▴ 50
Recent Replies
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…
Comment: Question regarding WGCNA by andres.firrincieli 3.6k
the within-group variability is so small that these look like technical replicates rather than independent biological replicates
Traffic: 2664 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