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q-value threshold for omics data when performing univariate cox analysis
MachineLearning q-value Cox FDR omics
3 hours ago by Yugan Gogul Muthukumar ▴ 10
1
vote
2
replies
121
views
Cross-species differential gene expression, finding orthologs
orthologs xSpecies stringtie Differential-expression
updated 5 hours ago by ★ 1.1k • written 11 hours ago by ▴ 10
0
votes
1
reply
74
views
Unexpected negative correlation between gene-length and counts
rna-seq bias normalisation
updated 6 hours ago by 88k • written 7 hours ago by ▴ 20
0
votes
0
replies
52
views
NGS clean UP PCR
NGS clean PCR UP
9 hours ago by Hassan • 0
837
votes
170
replies
177k
views
112 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 20 days ago by 3.5k • written 8.5 years ago by 102k
0
votes
1
reply
120
views
Perturb seq
perturbseq
updated 17 hours ago by 151k • written 23 hours ago by • 0
4
votes
4
replies
1.1k
views
Where can I find somatic whole-genome or exome FASTQ files (from tumor samples) with validated variants and corresponding VCFs publicly available?
fastq NGS pipeline INDELs SNVs
updated 14 hours ago by 151k • written 4 days ago by • 0
0
votes
0
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130
views
How important are allele fractions when calling variants?
GATK bacteria BCFTools
1 day ago by andean • 0
0
votes
0
replies
144
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Job: Two postdoctoral positions in generative AI and blood-based cancer detection, Aarhus University, Denmark
nucleosomes post_doc cancer_detection generativeAI bioinformatics
8 hours ago by Jakob Skou • 0
0
votes
2
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1.6k
views
Analysing Problem Seen In MEGA X
Alignment MEGAX Muscle
updated 1 day ago by • 0 • written 3.6 years ago by • 0
0
votes
0
replies
158
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discrepancies in ORA results between g:Profiler (gost) and clusterProfiler (enrichGO)
Analysis Enrichment
written 2 days ago by • 0
0
votes
0
replies
132
views
DESeq2 outliers-should I be concerned?
deseq2
2 days ago by bioinfo ▴ 150
0
votes
2
replies
293
views
Trimmomatic command
STAR RNASeq Trimmomatic
updated 2 days ago by 14k • written 3 days ago by ▴ 60
1
vote
1
reply
223
views
Blog: Setaria Pan-Genome Variation: Unraveling the Story of Domestication
pan-genome
updated 2 days ago by ★ 4.2k • written 3 days ago by ▴ 510
4
votes
9
replies
992
views
Facing issue with output of nextflow pipeline
output nextflow fastqc issue
updated 20 hours ago by 7.4k • written 6 weeks ago by ▴ 20
4
votes
2
replies
261
views
Forum: Pie Charts: to use or not to use
pie-chart graphs
updated 2 days ago by 22k • written 2 days ago by • 0
1
vote
1
reply
193
views
Minimum Number of Cells for Downstream Analysis after subsetting a particular cell type (scRNAseq)?
cell single
updated 2 days ago by 88k • written 2 days ago by ▴ 10
0
votes
3
replies
424
views
Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Acinetobacter guillouiae
nif NCBI_genome_database Acinetobacter_guillouiae Nitrogenase Nitrogen_fixation
updated 2 days ago by 151k • written 3 days ago by • 0
0
votes
1
reply
197
views
Target prediction
protien prediction Target
updated 2 days ago by ★ 3.0k • written 2 days ago by • 0
6
votes
12
replies
771
views
Heatmap of a transformed deseq object with pheatmap
deseq2 pheatmap
3 days ago by caroline.zanchi • 0
0
votes
0
replies
144
views
CNVkit CNVs call with threshold issues
CNVkit threshold_log2 Somatic_variant
3 days ago by AIMAR ▴ 10
2
votes
2
replies
292
views
PRS result interpretation
risk score PRS interpretation polygenic
3 days ago by trkfs ▴ 10
1
vote
0
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160
views
Several errors in DROP Workflow
DROP aberrantSplicing FRASER RNAseq
2 days ago by n_navy ▴ 10
2
votes
1
reply
233
views
More rare variants than common variants
PLINK GWAS
updated 3 days ago by 4.9k • written 4 days ago by ▴ 20
1
vote
1
reply
276
views
Question about vg giraffe, vg surject and Visualization tool for mapping result
vg
updated 4 days ago by ▴ 740 • written 5 days ago by • 0
0
votes
0
replies
190
views
Job: Postdoctoral Fellow in Machine Learning and Computational Biology, The University of Memphis
PTSD learning bioinformatics deep genomics
4 days ago by bjdaigle ▴ 10
5
votes
4
replies
582
views
Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness?
Replicates Omics Pooling
updated 4 days ago by 4.9k • written 9 days ago by • 0
2
votes
1
reply
269
views
Regressing variables for finding Differentially expressed genes
batcheffect seurat bias scRNASeq
updated 4 days ago by 6.3k • written 4 days ago by ▴ 390
0
votes
0
replies
230
views
Job: Head of Bioinformatics Facility (m/f/div) at Max Planck Institute of Epigenetics
germany e14
4 days ago by elsalatino • 0
2
votes
1
reply
278
views
GSEA and Cytoscape Enrichment maps
Cytoscape RNA-seq GSEA
updated 4 days ago by 6.3k • written 5 days ago by • 0
1
vote
1
reply
307
views
Alternatives to WGCNA
WGCNA
updated 5 days ago by 4.9k • written 5 days ago by ▴ 10
8
votes
4
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470
views
RNA-seq analysis
Htseq-count HiSat2 featurecounts STAR
updated 3 days ago by ★ 8.1k • written 5 days ago by • 0
2
votes
2
replies
1.3k
views
Liquid Biopsy datasets
RNA-Seq next-gen liquid biopsy miRNA cDNA
updated 5 days ago by ▴ 80 • written 4.7 years ago by • 0
1
vote
4
replies
1.1k
views
RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values.
RNA
updated 5 days ago by ▴ 80 • written 10 months ago by • 0
4
votes
3
replies
1.1k
views
Metagenomics mock datasets
metagenomics
updated 5 days ago by ▴ 80 • written 16 months ago by • 0
3
votes
0
replies
249
views
News: NCBI Comparative Genomics Virtual Codeathon, Sept 8-10.
genomics NCBI codeathon
4 days ago by MirianT_NCBI ▴ 800
1
vote
1
reply
277
views
Using structure prediction approaches to predict interaction between two proteins
protein prediction structure
updated 5 days ago by ★ 29k • written 6 days ago by ▴ 30
3
votes
3
replies
360
views
How to visualize Combat-seq corrected counts
batch-correction combat-seq
2 days ago by ybw8gh • 0
3
votes
6
replies
457
views
Single cell expression and accessibility integration using cellxgene data
cellxgene
4 days ago by 1769mkc ★ 1.3k
0
votes
1
reply
307
views
Umbrella pathways in KEGG
KEGG R
updated 5 days ago by 3.3k • written 6 days ago by ▴ 540
0
votes
2
replies
266
views
Peptide protein dynamics
Pepdide
updated 5 days ago by 15k • written 5 days ago by • 0
2
votes
4
replies
389
views
variant calling chromosome-wise from WGS data
wgs
updated 4 days ago by 151k • written 5 days ago by ▴ 60
5
votes
5
replies
384
views
Design matrix with uneven patient representation across stages
RNA-seq design-matrix limma
5 days ago by Lucas • 0
1
vote
2
replies
319
views
Forum: The best LLM or any tool to generate legal regex expression string for specific usage?
regex awk sed commands linux
updated 5 days ago by 151k • written 5 days ago by ▴ 140
3
votes
6
replies
2.2k
views
6 follow
minimap2 gets killed, but it doesn't explain why
minimap2
updated 5 days ago by 3.3k • written 14 months ago by ▴ 200
0
votes
1
reply
263
views
Reference-guided transcriptome assembly using multiple SRA experiments ?
assembly Transcriptome projects SRA
updated 4 days ago by 15k • written 5 days ago by ▴ 270
6
votes
10
replies
2.9k
views
Minimap2 error in Flye de novo assembly
Flye Minimap2
5 days ago by Nilo ▴ 20
0
votes
0
replies
297
views
How to find hormone related proteins from a list of gene/proteins
R
updated 5 days ago by 45k • written 6 days ago by ▴ 860
0
votes
0
replies
305
views
mtDNA variants from WGS data
mitogenome WGS
updated 5 days ago by 45k • written 6 days ago by • 0
0
votes
1
reply
278
views
Merge 1000 Genome gentotype AND genotype likelihood VCFs together
VCF LiftoverVcf Merge
updated 6 days ago by ▴ 630 • written 6 days ago by ▴ 240
121,197 results • Page 1 of 2424
Recent Votes
A: Criteria That Befit A Good Bioinformatics Phd Research
Merged CRAM output
Cross-species differential gene expression, finding orthologs
Comment: Where can I find somatic whole-genome or exome FASTQ files (from tumor samples)
Copy Number Variants with CNVKit
Answer: Detection SNPs and Indels Bacteria
Answer: Where can I find somatic whole-genome or exome FASTQ files (from tumor samples)
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Answer: Cross-species differential gene expression, finding orthologs by cfos4698 ★ 1.1k
I faced this problem previously. While I can't comment here on the relevant merits of your suggested approach, I can outline what I did. In…
Comment: Unexpected negative correlation between gene-length and counts by ATpoint 88k
What do we see in the plots? What is "gene counts" (and on which scale is this, log2?) and what are the lines? Are these samples? Code for …
Comment: Cross-species differential gene expression, finding orthologs by Dunois ★ 2.9k
I am also interested in these questions. I hope some of the more experienced and/or knowledgeable members here respond.
Comment: Perturb seq by GenoMax 151k
While you wait for answers a search brought up this analysis workflow: https://satijalab.github.io/Mixscale/
Comment: Facing issue with output of nextflow pipeline by colindaven 7.4k
Yeah, this looks like a hack.This page has more standard patterns - https://nextflow-io.github.io/patterns/ - You don't need the `mkdir` …
Comment: Where can I find somatic whole-genome or exome FASTQ files (from tumor samples) by CHOCADAPASSADAEMCHOQ • 0
Thank you so much!! So kind!
Comment: Analysing Problem Seen In MEGA X by humarafique.1234 • 0
I'm also facing the same issue. Have you been able to find a way to fix it?
Comment: How to visualize Combat-seq corrected counts by ybw8gh • 0
Sorry, I accidentally used ComBat! ComBat-seq did not produce negative counts. Thanks for all the help!
Answer: Trimmomatic command by swbarnes2 14k
Keep in mind for RNASeq 1) if the library was done properly, it's very unlikely you have many fragments shorter than your read length. …
Comment: Setaria Pan-Genome Variation: Unraveling the Story of Domestication by cmdcolin ★ 4.2k
>de novo assembled 110 reference-grade genomes for cultivated Setaria accessions this type of routine de novo assembly of genomes is aweso…
Comment: Facing issue with output of nextflow pipeline by ATpoint 88k
It looks hacky. Maybe it "works" but should not be taken as inspiration I guess. Are you sure output could be redicted to other processed l…
Comment: Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Aci by GenoMax 151k
Have you considered the possibility that if no strains of Acinetobacter guillouiae available in NCBI show presence of nitrogen fixing genes…
Answer: Facing issue with output of nextflow pipeline by neng ▴ 50
This is a common issue that many learners encounter when working with Nextflow output management. 1. Use publishDir("${params.outdir}/..…
Comment: Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Aci by Nafi • 0
Yes, I have tested all of them. I guess NCBI does not have this particular strain.
Answer: Pie Charts: to use or not to use by Joe 22k
As with any visualisation method, there is a time and a place for them. They are often misused, or used when a different method would be be…
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