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693
views
How does PLINK work?
PLINK logisticRegression GWAS
4.0 years ago by L_to_the_m ▴ 10
2
votes
1
reply
903
views
How to create a new file containing contigs of a certain length from another contigs file
fasta minia
updated 2.4 years ago by 45k • written 4.0 years ago by ▴ 20
0
votes
0
replies
591
views
predixcan error
vcf predixcan
updated 2.4 years ago by 45k • written 4.0 years ago by ▴ 150
0
votes
0
replies
574
views
News: Last call for our online training course "Data visualization with Python"
Python
4.0 years ago by Physalia-courses ★ 2.6k
0
votes
0
replies
792
views
News: Online training - Genomic Prediction
Genomics
4.0 years ago by Physalia-courses ★ 2.6k
1
vote
2
replies
1.1k
views
Plotting chromosomes and target capture baits
plotting target_capture Hyb-Seq R
4.0 years ago by Begonia_pavonina ▴ 210
1
vote
1
reply
750
views
Problem of visualizing results of PPI network
analyst network Cytoscape
updated 4.0 years ago by ▴ 310 • written 4.0 years ago by ▴ 20
0
votes
0
replies
635
views
Cutoffs for Proxy Identification: D' and R^2
plink2
4.0 years ago by dec986 ▴ 380
5
votes
15
replies
4.2k
views
7 follow
DESeq2 normalization - Found Difference in values when calculated manually
DESeq2 normalization difference
4.0 years ago by Sandhiya ▴ 20
0
votes
1
reply
953
views
getting different value list from GATK gc content and CANOES
CNV GATK CANOES
updated 4.0 years ago by • 0 • written 6.1 years ago by • 0
0
votes
1
reply
842
views
How is better perform the analyze the somatic mutations? (the mutations of my interest gene)
somatic VCF annotation Oncoplot
updated 4.0 years ago by ★ 3.0k • written 4.0 years ago by • 0
1
vote
1
reply
921
views
How to load user-defined genome in IGV-webapp
IGV-WEBAPP IGV igv
updated 4.0 years ago by 153k • written 4.0 years ago by ▴ 60
2
votes
6
replies
1.7k
views
Statistics on RNAseq data
on Statistics data RNAseq
updated 4.0 years ago by ▴ 350 • written 4.0 years ago by ▴ 30
0
votes
0
replies
856
views
Job: Bioinformatics position at the spatial transcriptomics facility of Lyon (France)
single-cell spatial-transcriptomics
updated 2.7 years ago by 45k • written 4.0 years ago by • 0
1
vote
2
replies
1.4k
views
Error when opening CEL files in python
python
updated 4.0 years ago by ★ 1.6k • written 4.0 years ago by • 0
1
vote
2
replies
1.2k
views
Variant Allele Frequency
Cancer
updated 4.0 years ago by ★ 3.0k • written 4.0 years ago by ▴ 60
0
votes
4
replies
2.1k
views
Find NLS in list of proteins.
localization nuclear signal
updated 4.0 years ago by 22k • written 4.0 years ago by ▴ 60
1
vote
4
replies
1.5k
views
Multiple hypothesis correction with multiple gene sets
gene-set-enrichment GO multiple-test-correction GO-enrichment
updated 4.0 years ago by ★ 8.3k • written 4.0 years ago by • 0
0
votes
2
replies
1.6k
views
HRD score LST?
cnv
updated 4.0 years ago by ★ 1.1k • written 4.9 years ago by ▴ 90
2
votes
2
replies
1.0k
views
Sudden coverage increase in IGV
IGV sequencing coverage
updated 4.0 years ago by • 0 • written 4.0 years ago by • 0
1
vote
2
replies
1.2k
views
How to get all genes and their annotations within a LD block?
GWAS haplotype SNPs genome wheat Ensembl
4.0 years ago by b.g.tamang ▴ 20
0
votes
2
replies
3.6k
views
From Bismark to methylkit, which file is better to use?
Bisulfite sequencing Bismark methylkit
updated 11 months ago by ★ 1.2k • written 4.7 years ago by ▴ 130
0
votes
1
reply
698
views
Regarding functional similarity analysis by GOSemSim package of R
GOSemSim
updated 4.0 years ago by 27k • written 4.0 years ago by • 0
0
votes
2
replies
1.8k
views
trinity run_DE_analysis.pl Failed with error: ‘package ‘limma’ could not be loaded’
run_DE_analysis.pl trinity
4.0 years ago by Rajesh ▴ 10
2
votes
4
replies
2.2k
views
Any suggestion on metagenomics pipelines for processing shotgun metagenomics whole genome sequencing samples?
metagenomics_pipelines WGS shotgun_metagenomics antimicrobial_resistance
4.0 years ago by eli_bayat ▴ 100
1
vote
3
replies
2.0k
views
WGCNA
Installation WGCNA
updated 4.0 years ago by ▴ 940 • written 4.0 years ago by ▴ 10
0
votes
0
replies
628
views
Neighboring index between clusters on a map
connectivity clustering
4.0 years ago by thejustpark ▴ 80
2
votes
3
replies
2.3k
views
GIAB Benchmark (High Confidence) Bed Filles
SNPS GIAB variants
updated 4.0 years ago by ▴ 290 • written 4.0 years ago by ▴ 840
8
votes
10
replies
4.9k
views
UCSC knownCanonical hg19 vs. hg38
genome UCSC hg19 hg38 canonical
updated 4.0 years ago by ▴ 670 • written 4.5 years ago by ▴ 150
1
vote
2
replies
1.3k
views
Tool: krust: a k-mer counter in Rust using the rust-bio and rayon crates
Rust kmer-counting fasta kmer
updated 4.0 years ago by 103k • written 4.0 years ago by ▴ 10
0
votes
2
replies
929
views
Can i estimate the hormone-receptor binding affinity ?
hormone
updated 2.4 years ago by 45k • written 4.0 years ago by • 0
1
vote
2
replies
980
views
Edit vcf file 0|0 to 0
linux vcf genomics edit
4.0 years ago by zoubda • 0
2
votes
4
replies
1.9k
views
Problem with BAM file headers
SAM GATK BAM
4.0 years ago by Lucas • 0
0
votes
0
replies
816
views
Weird PCA plot using WGCNA results
cancer PCA expression WGCNA plot
4.0 years ago by seta ★ 1.9k
0
votes
1
reply
1.1k
views
List of codon numbers in a panel
browser codon list ucsc genome
updated 4.0 years ago by ▴ 670 • written 4.4 years ago by • 0
2
votes
6
replies
4.2k
views
GenomeInfoDb (in R) and UCSC just stopped co-operating in terms of mm10
seqlevels seqlevelsStyle GenomeInfoDnb R UCSC
updated 4.0 years ago by 36k • written 4.2 years ago by ▴ 20
1
vote
3
replies
2.4k
views
clusterProfiler: number of GO terms in results
clusterProfiler
4.0 years ago by thistleq777 ▴ 10
2
votes
2
replies
1.8k
views
PRSice-2 without Ref SNP ID
Catalog PGS PRSice PRS
4.0 years ago by Jenish ▴ 20
0
votes
0
replies
523
views
How to do virtual screening and determining pharmacore
QSAR Docking
4.0 years ago by ashwing.kofficial ▴ 10
8
votes
3
replies
4.1k
views
Please help me understand linkage disequilibrium
LD Linkage disequilibrium SNP
updated 4.0 years ago by 22k • written 4.0 years ago by ▴ 60
0
votes
0
replies
1.2k
views
Job: PhD student for a computational breast cancer research project
Cancer PhD Omics
updated 2.5 years ago by 45k • written 4.0 years ago by • 0
1
vote
1
reply
2.1k
views
Ensembl VEP Docker: cannot write to FASTA lockfile
Ensembl Docker VEP
updated 4.0 years ago by 24k • written 4.0 years ago by • 0
0
votes
0
replies
716
views
How to show intermolecular forces between two chains within the same protein in Pymol
protein python pymol antibody antigen
4.0 years ago by Lucy • 0
2
votes
2
replies
1.5k
views
network analysis for microbial amplicon sequencing data
plot Network igraph R
4.0 years ago by Bioinfonext ▴ 470
0
votes
2
replies
1.6k
views
Unicycler and GNU parallel
Unicycler parallel
4.0 years ago by emma.a ▴ 130
0
votes
1
reply
3.0k
views
PROVEAN input script
python provean variant effect prediction
updated 4.0 years ago by • 0 • written 8.0 years ago by ▴ 10
0
votes
0
replies
669
views
GREAT genome ontology top hits criteria?
bed GREAT gene-ontology go
updated 2.5 years ago by 45k • written 4.0 years ago by ▴ 40
0
votes
0
replies
662
views
Job: Postdoctoral Scientist in Statistical Bioinformatics and Software Development, WEHI, Melbourne, Australia
Australia
4.0 years ago by Gordon Smyth ★ 8.3k
0
votes
0
replies
793
views
GREAT difference between 'mouse phenotype' and 'mouse phenotype single KO'
bed gene-ontology GREAT go
updated 2.5 years ago by 45k • written 4.0 years ago by ▴ 40
0
votes
1
reply
945
views
Running htseq-count to "grab" long non coding gene_id names
lncRNA htseq
updated 4.0 years ago by 153k • written 4.0 years ago by ▴ 210
121,793 results • Page 577 of 2436
Recent Votes
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
A: fgsea: What does fgseaMultilevel argument sampleSize mean/when to change it?
A: fgsea: What does fgseaMultilevel argument sampleSize mean/when to change it?
Custom Selection of GO Terms or Pathways in EnrichR Output
A: What is the difference between NZ_ and NC_ identifiers at NCBI?
Answer: Add NES value to GSEA plot
Add NES value to GSEA plot
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Recent Replies
Answer: How to obtain a refFlat file for the Rat by GenoMax 153k
Please don't ask the same question again in a new thread. This was answered a few weeks back: https://www.biostars.org/p/9613666/#9613671 …
Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful? by benformatics 4.1k
Usually it is not very useful. The only situation where it makes sense to use is where you do a gradient treatment (e.g. 0M, 5M, 50M, et…
Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful? by ATpoint 89k
No, don't rely on numbers. This can and is strongly influences by the sample size and noise, and by this power. Even at same sample size it…
Comment: Pseudobulk analysis using AggregateExpression() by adhisadi • 0
Hi, Did you figure this out? In my data some gene expressed in very low number of cells (less than 1% of total cells) appear as differentia…
Answer: Is a direct comparison of the number of up- and down-regulated genes meaningful? by kalavattam ▴ 370
*“Within a single experiment”* is O.K. with caveats. Comparing the number up versus the number down inside a single, well-designed experime…
Comment: Is a direct comparison of the number of up- and down-regulated genes meaningful? by GenoMax 153k
What do you mean by "directly compare"? Actual number of genes in the two groups don't have a special meaning. They will change based on …
Comment: RNA seq batch correction with technical replicates by Li • 0
Samples for condition B were made into two different sets of libraries for batch 1 and 2. The person who did the experiment has left, so I …
Comment: CUT&Tag signal normalization for generating bigWig files by ATpoint 89k
I would ignore the IgGs and only use it during peak calling. For the IP samples I would do https://www.biostars.org/p/413626/#414440
Comment: CUT&Tag signal normalization for generating bigWig files by RD ▴ 20
CUT&Tag shares protocol similarities with ATAC-seq, so I'd recommend using RPGC normalization via DeepTools. You might also consider testin…
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by swbarnes2 15k
You generally can't correct for replicates in such a tiny experiment like this, so I'd drop that element. But yes, if you want to do an …
Comment: BLAST Database error: Database memory map file error by goubert.clement ▴ 30
This is the way
Answer: How to detect divergent domains in AlphaFold models (CDD/InterProscan not workin by Mensur Dlakic ★ 29k
There isn't much beyond InterPro and CDD that would automatically detect divergent domains, as those databases already include almost all o…
Comment: Web Scraping and Text Analysis in R (March 21st - April 11th, 2025) Course by Ram 45k
That's a good approach. Personally, I copy-paste text and then extract info from that text file - you can see how prohibitive it can be to …
Comment: Dragon Motif Builder download link by colindaven 7.8k
Good points. More alternatives with more permissive licenses - https://github.com/jmschrei/memesuite-lite - https://github.com/jmschrei/…
Comment: bamCoverage with DNAse-seq shift by vivekbhr ▴ 700
Yes indeed if you just need the start of your DNAse protected fragment, use `--offset 1`
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