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Minimum number of samples for multi-omics data integration
integration data multi-omics
2 hours ago by Tundup • 0
0
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0
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53
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Editing and Adding to a GTF file
Annotation Gene GTF ID
6 hours ago by Keem Uarren Eiryll • 0
1
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0
replies
71
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News: Workshop: Virtual Genome Annotation, May 27–29
GenomeAnnotation workshop UConn
10 hours ago by zsc25001 ▴ 10
1
vote
1
reply
97
views
Assigning a string variable on Visual Studio using python
python variables visual studio
updated 8 hours ago by 151k • written 11 hours ago by • 0
836
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170
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175k
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112 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 8 days ago by 3.5k • written 8.4 years ago by 102k
0
votes
1
reply
107
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Tool: Gene Exons Painter
Genomics Visualisation Exons Transcripts Isoforms
updated 6 hours ago by ★ 29k • written 12 hours ago by ▴ 60
0
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0
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72
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News: Course online:Functional programming in R, May 27-30
R programming functional
16 hours ago by soledad.esteban • 0
2
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1
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127
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Herald: The Biostar Herald for Monday, May 05, 2025
herald
updated 13 hours ago by ★ 4.2k • written 16 hours ago by 3.5k
0
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0
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62
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How to generate .AED files from .CEL files using Linux (Affymetrix CytoScan HT-CMA 96F)
HT-CMA-96 analysis data affymetrix microarray
18 hours ago by genetixs ▴ 20
1
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7
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249
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ggplot make boxplots more wide
ggplot2 r
updated 12 hours ago by 12k • written 18 hours ago by ▴ 90
0
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0
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74
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News: Online course - Introduction to GWAS
R GWAS Statistics
20 hours ago by Physalia-courses ★ 2.6k
4
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3
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143
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Sample level genotype mapping in plink vcf output
VCF
updated 30 minutes ago by 166k • written 1 day ago by ★ 1.3k
6
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2
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209
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Tool: RNAseq Power Calculator
calculator Replicates RNAseq Statistics Power
1 day ago by Rafal ▴ 60
1
vote
1
reply
161
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Association (Protein interaction) in Intact database results what can really mean?
protein-protein-interaction database protein proteins Intact
updated 13 hours ago by ★ 29k • written 1 day ago by • 0
0
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0
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95
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Finding ploidy level from aneuploid NGS data having polypolidy level ranging from 8 to 12.
ploidy
1 day ago by analyst ▴ 60
0
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3
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283
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About FastP Tool
Raw Quality_control Preprocessing alignment reads
updated 16 hours ago by 151k • written 2 days ago by • 0
2
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7
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473
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Transcript identification and quantification
splitseq transcript scRNA
updated 5 hours ago by ★ 7.5k • written 3 days ago by • 0
0
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1
reply
188
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Treatment of nanoparticles after buying before the experiment
fermentation treatment Nanoparticles dark
updated 3 days ago by 88k • written 3 days ago by • 0
2
votes
1
reply
197
views
Tool: Accessible color palettes for charts and dataviz
dataviz
updated 23 hours ago by 6.2k • written 3 days ago by ▴ 20
3
votes
4
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294
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Warning in bcftools when subsetting a VCF by variant ID
bcftools VCF Beagle5.5
updated 30 minutes ago by 166k • written 3 days ago by • 0
1
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2
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235
views
Lucidea Array Spotter - Question about machinery
sequencing Microarray
updated 3 days ago by 151k • written 3 days ago by • 0
2
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2
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239
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Deduplication rate of shotgun metagenomes using fastqc
metagenome fastqc shotgun deduplication
updated 3 days ago by 151k • written 3 days ago by • 0
0
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3
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316
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Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
slingshot PCA Seurat scater single-cell
updated 3 days ago by 6.2k • written 3 days ago by ▴ 210
1
vote
1
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213
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What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
motifs atac-seq factor jaspar transcription
updated 3 days ago by 151k • written 4 days ago by • 0
0
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3
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296
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How can I find KO IDs for ORF sequences in a large FASTA file?
KEGG ORF
updated 3 days ago by 45k • written 4 days ago by • 0
0
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0
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173
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Single MAG Recruitment to multiple metaT Samples
metagenomics rna-seq transcriptomics
4 days ago by zjhennin • 0
0
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1
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1.0k
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Normalization - Tissue specificity analysis
gtex
updated 4 days ago by • 0 • written 4.1 years ago by ▴ 100
2
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4
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3.0k
views
Transcript Specific Expression Data
rna-seq
updated 4 days ago by • 0 • written 12.5 years ago by ▴ 30
9
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6
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7.9k
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6 follow
Database To Look For Tissue-Specific Transcript Expression Of The Same Gene.
transcript
updated 4 days ago by • 0 • written 12.2 years ago by ▴ 800
6
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6
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2.1k
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6 follow
Tool: Bioinformatics Docker Images Project (https://pegi3s.github.io/dockerfiles/)
containers docker
updated 1 day ago by ★ 2.4k • written 6.2 years ago by ▴ 10
1
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0
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241
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Job: Looking for a mentor
health mentor informatics
updated 4 days ago by 151k • written 4 days ago by ▴ 10
0
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0
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223
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Job: Postdoc fellow - genetics, proteomics, single cell and bioinformatics, Indiana University, Indianapolis, USA
proteomics genetics cell single bioinformatics
updated 4 days ago by 151k • written 4 days ago by • 0
0
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0
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196
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Strand bias and placement bias in variant calls
Variant filter
updated 4 days ago by 166k • written 4 days ago by • 0
0
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0
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199
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STARsolo for multiome GEX: trimming (--clip5pNbases) & whitelist handling
STARSolo multiome whitelist clip5pNbases
5 days ago by IrK ▴ 100
1
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8
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449
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Featurecounts: Unexpected number of features
featurecounts
4 days ago by JourneyToAbyss ▴ 240
4
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13
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10k
views
7 follow
GVSA: problem with gene identifier
gvsa RNA-Seq gsea
updated 5 days ago by • 0 • written 8.1 years ago by ▴ 10
0
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0
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200
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News: Workshop: Virtual Variant Detection, May 20-22
VariantDetection Workshop UConn
5 days ago by zsc25001 ▴ 10
1
vote
3
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354
views
Best way to combine biological replicate peaks?
ATAC-seq
updated 5 days ago by ★ 18k • written 6 days ago by • 0
1
vote
5
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381
views
Filtering HMMSCAN Domtblout Output when using Metagenomic Sequence as Input
hmmscan sequences domtblout metagenomic
updated 5 days ago by ★ 29k • written 5 days ago by • 0
0
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1
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275
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I have doubts regarding conducting meta-analysis of differentially expressed genes
meta-analysis Differential-Gene-Expression
updated 5 days ago by 4.9k • written 5 days ago by • 0
0
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3
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321
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Create local Blast database alias with blastdb_aliastool fails
blast
updated 3 days ago by 151k • written 5 days ago by • 0
2
votes
2
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355
views
Why is this interaction result not significant in DESeq2
DEG DE interaction DESeq2 RNA-seq
updated 5 days ago by ▴ 760 • written 6 days ago by ▴ 10
0
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0
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209
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Combining scRNA-seq datasets that have been processed differently
immunology Seurat
5 days ago by S • 0
6
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8
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13k
views
7 follow
WGCNA package in R: dendogram plot error
wgcna R
updated 5 days ago by 151k • written 8.3 years ago by ▴ 40
1
vote
1
reply
265
views
Problem with galaxy's Maxquant
Proteomics Maxquant Galaxy
updated 5 days ago by 151k • written 5 days ago by ▴ 10
0
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0
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211
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Workflow for DE after high-resolution CibersortX deconvolution
CibersortX Deconvolution
5 days ago by Aspire ▴ 380
0
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0
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210
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Is there any way to treat antibody titers as continuous data for microbiome analysis?
antibody-titers immunology microbiome
5 days ago by nmarin • 0
0
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0
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1.3k
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How to analyze transcriptional trends over time from multiple RNA-seq datasets with similar but not identical conditions?
pathway-analysis rnaseq differential-expression meta-analysis time-series
5 days ago by enee ▴ 20
0
votes
0
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205
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News: 9th Berlin Summer School in NGS Data Analysis 2025 (June 30 - July 4, 2025) -- SUMMER IN BERLIN --
Workshop RNA-Seq transcriptomics VariantCalling DNA-Seq
5 days ago by ecSeq Bioinformatics ▴ 20
55
votes
11
replies
49k
views
When and why is bwa aln better then bwa mem?
aln comparison bwa mem
5 days ago by dariober 15k
121,112 results • Page 1 of 2423
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Comment: Sample level genotype mapping in plink vcf output
Answer: When and why is bwa aln better then bwa mem?
Answer: When and why is bwa aln better then bwa mem?
Workshop: Virtual Genome Annotation, May 27–29
Comment: Transcript identification and quantification
Answer: Assigning a string variable on Visual Studio using python
Answer: Transcript identification and quantification
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Comment: Warning in bcftools when subsetting a VCF by variant ID by Pierre Lindenbaum 166k
cross-posted: https://bioinformatics.stackexchange.com/questions/23393/
Comment: Sample level genotype mapping in plink vcf output by Pierre Lindenbaum 166k
0 : REF 1: first ALT 2: second ALT 3 : third ALT etc...
Comment: Sample level genotype mapping in plink vcf output by 1769mkc ★ 1.3k
It works, how does this convert the binary to actual genotype?
Comment: Transcript identification and quantification by dsull ★ 7.5k
AH perfect!! Thanks -- that's exactly right! Here's the updated command (and links) for v3: pip install kb_python wget https://ra…
Comment: Gene Exons Painter by Mensur Dlakic ★ 29k
I am really not picking up on you - really. It just strikes me that if you want to get people to use your tools, a little bit more effort i…
Answer: Assigning a string variable on Visual Studio using python by GenoMax 151k
Not sure what you are trying to do here. How are the two lines you wrote above connected? You can't have a space in python variable names, …
Comment: Transcript identification and quantification by GenoMax 151k
There are some barcodes provided here --> https://github.com/mortazavilab/parse_pipeline/tree/main/barcodes Perhaps @dsull knows if there…
Comment: Ggplot make boxplots more wide by zx8754 12k
Set colour to Day as well: ```R ggplot( data = metadata, aes(x = location, y = gene, fill = Day, colour = Day)) + geom_boxplot() ``` To …
Comment: Transcript identification and quantification by dsull ★ 7.5k
Ooh, that's a bit tricky. I worked with v3 of the kit a while back but for some reason I can only find the R2/R3 barcodes. I'll let you kno…
Comment: The Biostar Herald for Monday, May 05, 2025 by cmdcolin ★ 4.2k
BinSeq format from ArcInstitute also ! https://github.com/ArcInstitute/binseq ...the trio of binseq+xsra+https://github.com/ArcInstitute/SR…
Comment: Transcript identification and quantification by anton.avramov • 0
Thank you for your help. We’re using v3 chemistry—do you know where I can obtain the barcode sequences? I don’t believe Parse shares them d…
Comment: Transcript identification and quantification by anton.avramov • 0
Thanks for the reply! I do use Parse pipeline to get expression matrices but what I really want to do is to be able to identify the transcr…
Comment: About FastP Tool by GenoMax 151k
Look at your alignment file records (with `samtools view` and such) and check the 6th field (`CIGAR` strings are described on page 8 in SAM…
Comment: Ggplot make boxplots more wide by Bastien Hervé 6.2k
https://ggplot2.tidyverse.org/reference/geom_dotplot.html
Comment: Ggplot make boxplots more wide by ATpoint 88k
`geom="point"` to make it a dot.
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