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122,231 results • Page 6 of 2445
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636
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MDS file NaN values
missing genome MDS
updated 25 days ago by ★ 90k • written 4 months ago by ▴ 60
0
votes
1
reply
1.1k
views
How to decide the normalization method for targeted metabolomics data ?
LC-MS normalization R metabolomics targeted-metabolomics
updated 25 days ago by ★ 90k • written 3 months ago by • 0
0
votes
1
reply
2.8k
views
Best Practice for Group Composition Plots in Phyloseq
phyloseq microbiome relative-abundance
updated 25 days ago by ★ 90k • written 3 months ago by ▴ 60
0
votes
3
replies
997
views
Sea of genomic wide significant hits in GWAS (Plink2) and Absence when using regenie
Genome-wide GWAS snps regenie plink2
updated 25 days ago by ★ 90k • written 5 weeks ago by • 0
2
votes
4
replies
1.9k
views
Can a spiked-in negative control still be considered a true negative control in 16S sequencing?
sequencing
updated 25 days ago by ★ 90k • written 5 weeks ago by • 0
0
votes
1
reply
627
views
useing lncHUB2 with R
Genelist lncHUB2 Rprograming lncRNAs
updated 25 days ago by ★ 90k • written 5 weeks ago by • 0
0
votes
1
reply
500
views
interpretation of the results obtained with digital PCR
dPCR
updated 25 days ago by ★ 90k • written 6 weeks ago by • 0
7
votes
17
replies
2.7k
views
A question of NGS requirement
storage RNAseq
11 days ago by zizigolu ★ 4.4k
1
vote
2
replies
408
views
Forum: How can I start learning bioinformatics? Any recommended beginner-friendly resources?
learning-resources beginners bioinformatics
13 days ago by dheeraj • 0
0
votes
1
reply
618
views
R code for getting TFs from ChEA2024 by gene list
TF ChEA2024 Rprograming Genelist
updated 25 days ago by ★ 90k • written 5 weeks ago by • 0
3
votes
3
replies
1.6k
views
install SCP problem
SCP
updated 25 days ago by ★ 90k • written 2.4 years ago by ▴ 140
0
votes
2
replies
856
views
exploring scRNA with only one sample per condition
scRNAseq exploring
updated 25 days ago by ★ 90k • written 5 weeks ago by • 0
1
vote
3
replies
858
views
Doubt on protein preparation before Vina
protein docking Vina doubt
updated 21 days ago by ★ 90k • written 5 weeks ago by • 0
0
votes
7
replies
1.0k
views
Upstream (5′) Coverage Depletion Observed in IGV
igv ont
updated 25 days ago by ★ 90k • written 5 weeks ago by ▴ 10
1
vote
5
replies
1.9k
views
Weird edgeR normalization results for one tissue
edgeR Normalization RNAseq
updated 25 days ago by ★ 90k • written 6 weeks ago by ▴ 10
0
votes
1
reply
596
views
Optimal way of running sysvi / scanvi
single-cell scanvi integration
updated 25 days ago by ★ 90k • written 5 weeks ago by 5.2k
1
vote
1
reply
508
views
Rescaling after relative abundance filtering of gut microbiome data
microbiome gut network
updated 25 days ago by ★ 90k • written 4 weeks ago by • 0
1
vote
5
replies
849
views
lollipop plot showing DNA sequence
mutation plot lollipop
updated 25 days ago by ★ 90k • written 4 weeks ago by • 0
4
votes
6
replies
852
views
Obtaining DESeq2 LFC values for Loadings of Principal Components
RNAseq Model DESeq2 Design PCA
20 days ago by Nishant • 0
0
votes
1
reply
340
views
Exploring cross-cancer similarity using SNP or variant data with deep learning
tcga deep-learning snp cancer
updated 25 days ago by ★ 90k • written 4 weeks ago by ▴ 30
0
votes
3
replies
605
views
Batch correction with ComBat for samples from multiple sampling sites
batch-correction ComBat
updated 25 days ago by ★ 90k • written 4 weeks ago by ▴ 20
0
votes
2
replies
357
views
Autosome/ sex chromosome assembly error
genomics analysis sexchromosome tools
updated 25 days ago by ★ 90k • written 28 days ago by • 0
1
vote
1
reply
599
views
How should I interpret GSEA results for the C6: Oncogenic Signatures collection (e.g., MYC_UP.V1_DN)?
RNA-seq Oncogenic MSigDB GSEA pathways
updated 25 days ago by ★ 90k • written 28 days ago by • 0
0
votes
2
replies
357
views
Polyadenylation-PAS sites APAlyzer
R package bioinformatics
updated 25 days ago by ★ 90k • written 28 days ago by ▴ 140
3
votes
3
replies
521
views
Mixed marker expression in Xenium data
Clustering Xenium explorer
updated 25 days ago by ★ 90k • written 27 days ago by ▴ 10
3
votes
3
replies
531
views
Help interpreting antiSMASH BGCs for EPA (eicosapentaenoic acid) biosynthesis
biosynthetic_gene_cluster secondary_metabolism PKS heterologous_expression
updated 25 days ago by ★ 90k • written 27 days ago by • 0
0
votes
1
reply
178
views
reference genome into chromosomes but annotation only at scaffolds level
reference rnaseq genome scaffolds annotation
updated 25 days ago by ★ 90k • written 25 days ago by • 0
0
votes
0
replies
187
views
News: Course: Multimodal AI for Systems Biology (Online, 2–6 March 2026)
Genomics multimodalAI MultiOmics
26 days ago by Physalia-courses ★ 2.7k
4
votes
4
replies
966
views
cufflinks- cuffquant issue
cufflinks
updated 26 days ago by 8.1k • written 20 months ago by • 0
1
vote
1
reply
277
views
Set parameters of fastsimcoal2.
fastsimcoal2
updated 26 days ago by 154k • written 26 days ago by • 0
2
votes
1
reply
325
views
Is it possible to reverse a VST transformation to obtain original counts?
bulkRNAseq VST-transformed_matrix
updated 27 days ago by 90k • written 27 days ago by • 0
4
votes
15
replies
6.2k
views
8 follow
Data retrieval from GEO
Microarray GEO
updated 27 days ago by 154k • written 8.3 years ago by ★ 1.4k
9
votes
2
replies
21k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
updated 27 days ago by • 0 • written 2.9 years ago by ▴ 520
0
votes
2
replies
876
views
News: Only 8 places left - 1st Berlin Winter School in RNA-Seq Data Analysis (Dec 8-11, 2025)
Transcriptomics RNA-Seq Expression Differential
27 days ago by ecSeq Bioinformatics ▴ 20
0
votes
0
replies
228
views
News: Workshop: Virtual Genome Annotation, November 18–20
GenomeAnnotation workshop UConn
27 days ago by zsc25001 ▴ 10
5
votes
5
replies
1.1k
views
hisat2 error-Paired end reads not equal or lack of RAM/disk space?
end fastq paired
updated 6 weeks ago by 90k • written 7 weeks ago by ▴ 140
47
votes
17
replies
17k
views
11 follow
Forum: Is Software Development a key part of Bioinformatics?
Software-Development
written 10.9 years ago by ▴ 70
1
vote
2
replies
444
views
deep learning architectures
Deep learning bioinformatics
updated 28 days ago by 5.2k • written 28 days ago by • 0
2
votes
1
reply
390
views
Creating a personalized genome assembly for read simulation from illumina WGS data
illumina consensus wgs phasing simulation
updated 28 days ago by 8.1k • written 29 days ago by ▴ 80
4
votes
5
replies
678
views
Prokaryotic RNA-seq: how to handle ncRNAs in featureCounts and DE analysis?
ncRNA lcRNA tRNA tmRNA
28 days ago by MaxMin ▴ 10
2
votes
1
reply
534
views
Unable to download bacterial protein sequences from NCBI using datasets CLI (DOMAIN is not a valid V2reportsRankType error)
prokaryotes datasets ncbi
updated 28 days ago by 154k • written 28 days ago by ▴ 40
0
votes
0
replies
205
views
News: Introduction to Nextflow online course
Reproducibility Nextflow training Workflow-Manager
28 days ago by Physalia-courses ★ 2.7k
3
votes
1
reply
297
views
Keep FastQC homopolymers or switch to fastp auto-detection?
Adapter
updated 28 days ago by 154k • written 28 days ago by • 0
1
vote
3
replies
522
views
Is there a term called 'pseudoenrichment' in Cut&Run analysis?
cutandrun chipseq
updated 28 days ago by 5.2k • written 29 days ago by • 0
2
votes
2
replies
370
views
Include plasmid sequences in RNA-seq differential expression analysis for bacteria?
RNA-SEQ rnaseq bacteria DE plasmid
updated 28 days ago by 154k • written 29 days ago by ▴ 10
0
votes
0
replies
238
views
Forum: For those with in autoimmune research, what are the biggest challenges seen in translating findings into real therapeutics?
drug-discovery autoimmune-disease immunology translational-research
29 days ago by greenandblackhack • 0
3
votes
2
replies
895
views
Nextflow error: “Invalid method invocation call with arguments (java.util.ArrayList)” when connecting processes via joined channels
homer chipseq nextflow
updated 29 days ago by 90k • written 4 weeks ago by ▴ 40
0
votes
0
replies
343
views
Blog: Introduction
introduction
updated 29 days ago by 45k • written 4 weeks ago by • 0
4
votes
2
replies
574
views
Assembling a chloroplast genome using only PacBio data (Illumina reads lost)
chloroplast genome-assembly
updated 4 weeks ago by ★ 1.8k • written 4 weeks ago by • 0
3
votes
4
replies
821
views
replicate SyRi/plotsr output plot in R
R SyRi synteny
4 weeks ago by Matteo Ungaro ▴ 140
122,231 results • Page 6 of 2445
Recent Votes
Answer: Chip-seq analysis Diffbind
Question about variant calling method using pangenome-graph
Comment: SyntaxError in file /snakefile, line 22: invalid decimal literal: None
Answer: Is this Rosalind inspired project actually useful?
Answer: Minimap2 segfaults when mapping Nanopore reads to a very large reference databas
Comment: How to normalize the intensity of bigwig files based on a group of house-keeping
Answer: Re-assembling old RNA-seq reads vs. using an existing transcriptome assembly
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Recent Replies
Comment: Chip-seq analysis Diffbind by Irene ▴ 10
Thank you very much for always answering my doubts and questions. I truly value and appreciate it because it helps me understand the result…
Comment: Minimap2 segfaults when mapping Nanopore reads to a very large reference databas by firefox91 ▴ 10
Many thanks !
Answer: Re-assembling old RNA-seq reads vs. using an existing transcriptome assembly by GenoMax 154k
> I have access to both the raw reads and the previously assembled transcriptome submitted to TSA. and > I am trying to determine wheth…
Answer: Re-assembling old RNA-seq reads vs. using an existing transcriptome assembly by dthorbur ★ 3.2k
There are a few factors to consider: **The quality of the existing reference.** If there is a high quality chromosome level assembly,…
Comment: "sortmerna" quitting early--is this is a memory issue? by colindaven 8.1k
Pls add the output and your system (especially RAM), no one here can guess.
Answer: Power calculations for differentially methylated DNA samples from sequencing by colindaven 8.1k
There are software packages for power analysis such as https://academic.oup.com/bioinformaticsadvances/article/5/1/vbaf150/8173951.
Comment: Data integration single cell using Harmony by Arup Ghosh 3.5k
Run QC for each sample separately, then merge run SCTransform, PCA, then Harmony, UMAP, FindNeighbors and FindClusters.
Comment: Data integration single cell using Harmony by _deb • 0
Thank you for the quick answer. I still have a doubt. It would be better to pre-process each sample separately (*filtering, SCTransform…
Comment: Issue while running Kenddata. by rana.elromh • 0
I checked the memory before executing this command. I made a bash script on Ubuntu to run it on 15 folders. But, this problem happened in f…
Comment: Prokka output genes clusterization by function by Mensur Dlakic ★ 30k
Many proteins have multiple domains, and are correctly classified with multiple KO numbers. That's not a bug in `kofam_scan` but rather a r…
Comment: mapping sequences on specific region of bacteria genome by samuel.a.odonnell ▴ 650
If you want to visualise the mapping; take a look at using IGV. It just requires the genome you used to map the reads and the BAM output (n…
Comment: Prokka output genes clusterization by function by shevch2009 ▴ 20
Thanks, I had completely forgotten that METABOLIC works with protein sequences. That will work :) I was just trying to figure out how peop…
Answer: Prokka output genes clusterization by function by Mensur Dlakic ★ 30k
It is easy to install `kofam_scan` and get the output: https://github.com/takaram/kofam_scan What is the impediment to using METABOLI…
Answer: Manual corrections for allele mismatches by curious ▴ 900
take a look at thomas winkler's stuff: https://www.nature.com/articles/nprot.2014.071
Comment: Repeated Coordinate Errors (>171823) in NC_007605.1 (EBV) GTF Conversion (LMP2A/ by halo22 ▴ 300
Thanks for sharing this. I was able to get makeref to work.
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