Limit : this week
all time today this week this month this year
367 results • Page 1 of 8
Sort: Votes
Rank Views Votes Replies
87
votes
24
replies
23k
views
17 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 1 day ago by • 0 • written 3.5 years ago by 3.2k
54
votes
12
replies
28k
views
12 follow
Out Of Disk Space With Picard Tools ?
picard
updated 21 hours ago by • 0 • written 12.0 years ago by ★ 2.9k
39
votes
9
replies
42k
views
6 follow
Batch effects : ComBat or removebatcheffects (limma package) ?
limma sva Combat batch-effect
updated 2 days ago by 43k • written 6.7 years ago by ★ 1.3k
34
votes
16
replies
20k
views
9 follow
Filtration Of Reads With Length Lower Than 30 From Bam
read length bam
updated 7 hours ago by ▴ 10 • written 10.2 years ago by ▴ 180
30
votes
12
replies
3.8k
views
Trying to understand the maths behind one Limma function
limma RNA-Seq batch-effect
updated 3 days ago by 43k • written 4.0 years ago by ▴ 330
23
votes
23
replies
9.8k
views
6 follow
How to see if adjusting batch effect in RNA-seq is working or not
RNA-Seq removeBatchEffect batch-effect edger
updated 1 day ago by 43k • written 5.3 years ago by ▴ 130
23
votes
11
replies
4.8k
views
7 follow
Code golf: detecting homopolymers of length N in the (human) genome
code golf fasta homopolymer repeat
updated 3 days ago by 43k • written 4.9 years ago by 47k
22
votes
18
replies
6.1k
views
about batch correction in scRNA-seq
scRNA scRNA-seq batch-effect
updated 21 hours ago by 43k • written 4.5 years ago by ★ 1.4k
15
votes
6
replies
1.2k
views
6 follow
VCF to human friendly form?
vcf visualization
updated 4 days ago by 161k • written 19 months ago by ▴ 10
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 2 days ago by 43k • written 6.8 years ago by ★ 1.3k
11
votes
9
replies
11k
views
10 follow
Genome assembly statistical tools
Assembly statistics
updated 6 days ago by • 0 • written 4.7 years ago by ▴ 10
11
votes
9
replies
6.9k
views
How to choose method to integrate different patient sample together in Seurat
Seurat scRNA batch-effect harmony
updated 1 day ago by 43k • written 4.2 years ago by ▴ 80
11
votes
12
replies
742
views
Downloaded pdb's on rcsb.org
rcsb pdb
updated 17 hours ago by 43k • written 23 hours ago by • 0
10
votes
7
replies
7.1k
views
6 follow
Convert GVF to VCF
vcf
updated 3 days ago by • 0 • written 9.2 years ago by ▴ 970
10
votes
36
replies
5.8k
views
Design in DESeq: Can you combine explicit and implicit batch effect correction in (SVA+Metadata Variables)?
SVA batch-effect DESeq2 R
updated 2 days ago by 43k • written 5.7 years ago by ▴ 620
10
votes
6
replies
14k
views
7 follow
How To Identify The 16S Rrna Gene Sequence In A Genome
updated 1 day ago by 6.3k • written 10.9 years ago by ▴ 10
9
votes
10
replies
4.4k
views
Using rnaseq reference sample across batches
RNA-Seq batch-effect
updated 2 days ago by 43k • written 7.4 years ago by ▴ 30
9
votes
3
replies
6.9k
views
EdgeR-GLMs correcting for batch effects
RNA-Seq edgeR Batch-Effect
updated 21 hours ago by 43k • written 9.9 years ago by ▴ 250
9
votes
10
replies
6.9k
views
Harmony batch correction vs. regressing out donor effect in Seurat
Seurat scRNA-seq Harmony RNA-seq batch-effect
updated 21 hours ago by 43k • written 4.5 years ago by ▴ 140
9
votes
12
replies
4.1k
views
Batch effect, how to create a model matrix
RNA-Seq deseq2 batch-effect
updated 1 day ago by 43k • written 4.9 years ago by ▴ 330
9
votes
4
replies
1.9k
views
Integration of RNA-Seq data with microarray data
microarray RNA-Seq batch-effect R
updated 2 days ago by 43k • written 4.0 years ago by ▴ 30
8
votes
6
replies
2.5k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 1 day ago by 3.0k • written 23 months ago by ▴ 230
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl repeat
updated 4 days ago by ▴ 190 • written 15 months ago by ★ 1.4k
8
votes
10
replies
661
views
bash script
whole-genome-sequencing
updated 3 days ago by 43k • written 11 days ago by ▴ 30
8
votes
12
replies
1.9k
views
Metric to use for RNAseq expression matrix
gene-expression TPM RNA-Seq counts batch-effect
1 day ago by Ram 43k
7
votes
3
replies
2.6k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
updated 8 hours ago by 6.3k • written 15 months ago by ▴ 130
7
votes
4
replies
1.4k
views
Is there any journal article to reference removeBatchEffect function from Limma?
batch removebatcheffect limma rna-seq batch-effect
updated 2 days ago by 43k • written 21 months ago by ▴ 20
7
votes
7
replies
519
views
Can you suggest a protein PDB that has two chainst but only 50 total number of atoms?
protein pdb protein-databank
updated 6 days ago by 4.5k • written 7 days ago by • 0
7
votes
4
replies
2.1k
views
filtering genes by pearson correlation
correlation RNA-Seq R
updated 2 days ago by 43k • written 6.0 years ago by ▴ 120
7
votes
10
replies
2.6k
views
6 follow
Batch effect correction to compare differentially expressed genes across datasets
batch batch-effect DESeq2 rna-seq
updated 2 days ago by 43k • written 2.0 years ago by ▴ 60
7
votes
7
replies
1.0k
views
Prediction tools summary - zero values
statistics
updated 2 days ago by • 0 • written 6 months ago by ▴ 50
7
votes
3
replies
4.5k
views
how to deal with batch effect in TCGA RNA-seq dataset
TCGA RNA-Seq batch-effect
updated 1 day ago by 43k • written 5.1 years ago by ▴ 100
7
votes
3
replies
1.2k
views
biomaRt::getSequence - Invalid type argument
biomaRt R
updated 2 days ago by 43k • written 3.8 years ago by ▴ 680
7
votes
5
replies
3.7k
views
ISCN annotation for SV/CN VCF files
SV
updated 1 day ago by • 0 • written 7 months ago by ▴ 50
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray meta-analysis DEG batch-effect
updated 1 day ago by 43k • written 4.8 years ago by ▴ 30
7
votes
2
replies
3.6k
views
Timeout on getBM() to retrieve snps from locations
biomaRt getBM R
updated 2 days ago by 43k • written 5.2 years ago by ▴ 600
7
votes
7
replies
839
views
Forum: Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career advice
updated 3 days ago by ★ 2.5k • written 4 days ago by • 0
7
votes
8
replies
630
views
Why are the basics so complicated? Basic coverage filtering for VCF files
filter vcf coverage
updated 6 days ago by ▴ 40 • written 10 days ago by ▴ 40
6
votes
10
replies
1.7k
views
Integration of Microarray datasets with different platforms and biological groups
limma microarray DEA batch-effect
updated 1 day ago by 43k • written 4.7 years ago by ▴ 60
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 21 hours ago by 43k • written 7.0 years ago by ▴ 80
6
votes
7
replies
1.6k
views
How to assess RNA-Seq batch correction success?
Combat RNA-Seq Limma DESeq2 batch-effect
updated 21 hours ago by 43k • written 4.9 years ago by ▴ 140
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq edgeR DESeq2 Batch-Effect
updated 2 days ago by 43k • written 5.2 years ago by ▴ 40
6
votes
11
replies
3.3k
views
Collapsing probesets to genes on WGCNA
WGCNA gene-expression R
updated 2 days ago by 43k • written 5.2 years ago by ▴ 120
6
votes
8
replies
471
views
BRAKER3 genome annotation
annotation BRAKER3 genome
updated 2 days ago by 14k • written 4 days ago by ▴ 40
6
votes
17
replies
6.5k
views
Can you add a label key to heatscatter plot in R?
heatscatter visualization R
updated 2 days ago by 43k • written 9.5 years ago by ▴ 100
6
votes
2
replies
1.5k
views
Writing a batch script for analyzing RNA-Seq data
RNA-Seq quantification alignment
updated 2 days ago by 43k • written 5.1 years ago by ▴ 250
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 2 days ago by • 0 • written 4.6 years ago by ▴ 40
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq batch batch-effect sequencing
updated 2 days ago by 43k • written 2.9 years ago by ▴ 60
5
votes
5
replies
837
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq Blacklist
updated 6 days ago by 43k • written 10 months ago by ▴ 30
5
votes
2
replies
1.0k
views
How to perform batch correction when we have only single condition?
sva combat batch-effect DESeq2
updated 2 days ago by 43k • written 3.7 years ago by ▴ 680
367 results • Page 1 of 8
Recent Votes
Answer: Illumina Read Stitching
Answer: Problem with Sniffles pipeline and SV calling help
Illumina reads preprocessing best practice for snp calling applications
Comment: Illumina reads preprocessing best practice for snp calling applications
Installing/switching between versions of R/Rstudio/Bioconductor
How To Generate Phylogeny Tree, Based On Snps?
How To Construct Phylogenetic Tree Using Snps
Recent Locations • All
ETH Zurich, just now
United States, just now
Marseille, 1 minute ago
Greenland, 2 minutes ago
United Kingdom, 3 minutes ago
Italy, 3 minutes ago
United States, 4 minutes ago
Recent Awards • All
Popular Question to DanielEB_fisk ▴ 20
Scholar to Pierre Lindenbaum 161k
Scholar to Dinmukhamed • 0
Popular Question to i.sudbery 19k
Popular Question to biwdpang • 0
Popular Question to Michael 54k
Scholar to Gordon Smyth ★ 7.0k
Recent Replies
Comment: Installing/switching between versions of R/Rstudio/Bioconductor by Ram 43k
Your tutorial required `sudo` and thus is not doable for a majority of people. Any alternative to `sudo snap`?
Comment: Should I apply doublet detection for each pool seperately? by Ram 43k
Do not delete posts that have received feedback,
Comment: QC exclusion of A/T or G/C alleles to avoid strand issues by _quantum_girl_ ▴ 10
They aren't merging any datasets. Just for reference the paper is this: https://www.nature.com/articles/s41380-022-01674-9#MOESM1. Citing: …
Comment: RNA seq differential expression analysis by BioinfGuru ★ 1.7k
https://help.galaxyproject.org/
Answer: RNA seq differential expression analysis by Mohamed Abderrahmane ▴ 10
The tool RSEM, which performs transcript quantification for RNA-Seq data, provides FPKM.
Comment: Illumina reads preprocessing best practice for snp calling applications by Enrique • 0
Hi! I'm still interested in the step that you use for the SNP calling. Did you use `trimmomatic` or another tool for trimming before mappin…
Comment: Could you please assist in identifying this cluster? by ATpoint 81k
The information do not suffice. Please show plots and identified marker genes. Also, make sure it is not a trash cluster with low number of…
Comment: Free/open source 23andme-like analysis by joe ▴ 510
Thank you, I added 'accurate' now ;) I'm surprised to find out that there isn't some tool like multiqc that just summarizes all this infor…
Comment: Memory usage of picard Samsort by ATpoint 81k
Guys, just use `samtools sort` which won't get you into trouble with any of that.
Comment: Ciriquant not configuring hisat2 indexed files by Carlo Yague 8.6k
I don't know for sure, but I think that decreasing the amount of threads (1 or 2 instead of 4) will decrease the memory requirements of the…
Answer: Memory usage of picard Samsort by tamas.malkocs • 0
For me, setting `TMP_DIR` (`--TMP_DIR /home/tmp`) didn't work in picard 2.21.1. What solved the issue was setting the environmental variabl…
Answer: Plink merge errors. by Dinmukhamed • 0
I found answer https://www.biostars.org/p/101191/.
Comment: Ciriquant not configuring hisat2 indexed files by Atul K. • 0
it worked. Thank you. Now my terminal is crashing, seems 16gb of RAM and 4 cores isn't enough. Can you suggest something?
Comment: Adding CB tag to bam file by Maria • 0
I checked Picard ```AddOrReplaceReadsGroups``` and ```AddOATag```. Is that what you're referring to?
Comment: Free/open source 23andme-like analysis by Michael 54k
Noted that 'accurate' wasn't among your criteria ;) Anyway, most variant callers are free open-source software. However, for ancestry ana…
Traffic: 2859 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