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Differeces between Seurat::RunPCA and scater::runPCA affect downstream analyses
slingshot PCA Seurat scater single-cell
56 minutes ago by txema.heredia ▴ 210
1
vote
0
replies
35
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What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
motifs atac-seq factor jaspar transcription
4 hours ago by Ambuj • 0
0
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1
reply
86
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How can I find KO IDs for ORF sequences in a large FASTA file?
Computational Biology Bioinformatics
updated 11 hours ago by ★ 29k • written 11 hours ago by • 0
0
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0
replies
59
views
Single MAG Recruitment to multiple metaT Samples
metagenomics rna-seq transcriptomics
11 hours ago by zjhennin • 0
0
votes
2
replies
887
views
Normalization - Tissue specificity analysis
gtex
updated 12 hours ago by • 0 • written 4.1 years ago by ▴ 100
836
votes
170
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175k
views
112 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 4 days ago by 3.5k • written 8.4 years ago by 102k
2
votes
4
replies
2.9k
views
Transcript Specific Expression Data
rna-seq
updated 12 hours ago by • 0 • written 12.5 years ago by ▴ 30
9
votes
6
replies
7.8k
views
6 follow
Database To Look For Tissue-Specific Transcript Expression Of The Same Gene.
transcript
updated 12 hours ago by • 0 • written 12.2 years ago by ▴ 800
6
votes
5
replies
1.9k
views
Tool: Bioinformatics Docker Images Project (https://pegi3s.github.io/dockerfiles/)
containers docker
updated 16 hours ago by 151k • written 6.2 years ago by ▴ 10
0
votes
0
replies
90
views
Job: Looking for a mentor
health mentor informatics
updated 16 hours ago by 151k • written 17 hours ago by • 0
0
votes
0
replies
88
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Job: Postdoc fellow - genetics, proteomics, single cell and bioinformatics, Indiana University, Indianapolis, USA
proteomics genetics cell single bioinformatics
updated 17 hours ago by 151k • written 18 hours ago by • 0
0
votes
0
replies
71
views
Job: Postdoc ML/AI and omics in Alzheimer disease at Indiana University (Indianapolis) USA
Alzheimer Omics Postdoc AI
18 hours ago by alwayshope ▴ 40
0
votes
0
replies
77
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Strand bias and placement bias in variant calls
Variant filter
updated 22 hours ago by 166k • written 1 day ago by • 0
0
votes
0
replies
86
views
STARsolo for multiome GEX: trimming (--clip5pNbases) & whitelist handling
STARSolo multiome whitelist clip5pNbases
1 day ago by IrK ▴ 100
1
vote
8
replies
274
views
Featurecounts: Unexpected number of features
featurecounts
15 hours ago by JourneyToAbyss ▴ 240
4
votes
13
replies
10k
views
7 follow
GVSA: problem with gene identifier
gvsa RNA-Seq gsea
updated 1 day ago by • 0 • written 8.0 years ago by ▴ 10
0
votes
0
replies
85
views
News: Workshop: Virtual Variant Detection, May 20-22
VariantDetection Workshop UConn
1 day ago by zsc25001 • 0
0
votes
0
replies
94
views
Plink vcf file output reporting
vcf
1 day ago by 1769mkc ★ 1.3k
1
vote
3
replies
220
views
Best way to combine biological replicate peaks?
ATAC-seq
updated 1 day ago by ★ 18k • written 2 days ago by • 0
1
vote
5
replies
239
views
Filtering HMMSCAN Domtblout Output when using Metagenomic Sequence as Input
hmmscan sequences domtblout metagenomic
updated 1 day ago by ★ 29k • written 1 day ago by • 0
0
votes
1
reply
154
views
I have doubts regarding conducting meta-analysis of differentially expressed genes
meta-analysis Differential-Gene-Expression
updated 1 day ago by 4.9k • written 2 days ago by • 0
0
votes
2
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141
views
Create local Blast database alias with blastdb_aliastool fails
blast
1 hour ago by etienne • 0
2
votes
2
replies
231
views
Why is this interaction result not significant in DESeq2
DEG DE interaction DESeq2 RNA-seq
updated 1 day ago by ▴ 760 • written 2 days ago by ▴ 10
0
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0
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96
views
Combining scRNA-seq datasets that have been processed differently
immunology Seurat
1 day ago by S • 0
6
votes
8
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12k
views
7 follow
WGCNA package in R: dendogram plot error
wgcna R
updated 1 day ago by 151k • written 8.3 years ago by ▴ 40
1
vote
1
reply
126
views
Problem with galaxy's Maxquant
Proteomics Maxquant Galaxy
updated 1 day ago by 151k • written 1 day ago by ▴ 10
0
votes
0
replies
101
views
Workflow for DE after high-resolution CibersortX deconvolution
CibersortX Deconvolution
1 day ago by Aspire ▴ 380
0
votes
0
replies
101
views
Is there any way to treat antibody titers as continuous data for microbiome analysis?
antibody-titers immunology microbiome
1 day ago by nmarin • 0
0
votes
0
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478
views
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
2 days ago by enee ▴ 20
0
votes
0
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97
views
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
2 days ago by ecSeq Bioinformatics ▴ 20
53
votes
11
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49k
views
When and why is bwa aln better then bwa mem?
aln comparison bwa mem
2 days ago by dariober 15k
0
votes
0
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100
views
How to deal polyploid and aneuploid sugarcane genome R570 for variant calling
aneuploid
2 days ago by analyst ▴ 60
0
votes
2
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177
views
False positives annotation of Augustus?
Augustus training
updated 2 days ago by 15k • written 2 days ago by • 0
1
vote
2
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265
views
Mapping SNPs to genes
biomart SNP ensembl r gene
2 days ago by Nigussie • 0
0
votes
2
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173
views
Rockhopper Reference Genome Error
Rockhopper
1 day ago by ATS • 0
0
votes
0
replies
116
views
What can cause Faststructure to produce really high K clusters as optimal (e.g. 12 - 14)
SNP vcf population
2 days ago by Drew ▴ 10
0
votes
7
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1.1k
views
Trouble finding datasets
GEO SRA
updated 2 days ago by ▴ 20 • written 18 months ago by ▴ 20
4
votes
2
replies
985
views
Imputation server failing to see samples in VCF files
imputation VCF
updated 2 days ago by • 0 • written 19 months ago by ▴ 10
0
votes
3
replies
216
views
Read Mapping of Reads to Reference Genome Shows Extreme Bias
mapping read bwa-mem coverage
updated 2 days ago by 55k • written 2 days ago by • 0
0
votes
0
replies
125
views
News: Introduction to Python for Biologists (IPYB01)
Python
updated 2 days ago by 151k • written 2 days ago by ▴ 110
0
votes
0
replies
123
views
News: Machine Learning using Python (MLUP01)
Python
updated 2 days ago by 151k • written 2 days ago by ▴ 110
2
votes
2
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208
views
Interpreting a vcf file
variant vcf
updated 16 hours ago by ★ 4.2k • written 2 days ago by ▴ 20
3
votes
0
replies
155
views
Herald: The Biostar Herald for Tuesday, April 29, 2025
herald
2 days ago by Biostar 3.5k
5
votes
2
replies
281
views
Best choices for DGE and pathway enrichment analysis in single cell data using pseudobulk?
DEG GSEA single-cell pseudobulk
1 hour ago by txema.heredia ▴ 210
6
votes
8
replies
2.6k
views
7 follow
Cluster annotation in single cell
Single-cell
updated 3 days ago by • 0 • written 20 months ago by ▴ 100
3
votes
6
replies
6.6k
views
Manual annotation of cell types in single cell RNA-seq
Seurat single_cell annotation
updated 3 days ago by • 0 • written 3.7 years ago by ▴ 240
3
votes
7
replies
374
views
Clustal Omega stand alone versus website percent identity matrix
clustal MSA identity percent
1 day ago by sorrymouse ▴ 120
0
votes
1
reply
223
views
PCA vs sparse PCA : differences in results
ML
updated 3 days ago by 45k • written 3 days ago by ▴ 20
0
votes
1
reply
454
views
Is this the correct DESeq2 design for model with interaction terms and batch effect and paired samples?
paired batch DESeq2 interaction
updated 2 days ago by 88k • written 3 days ago by • 0
0
votes
3
replies
2.3k
views
Has the TRON Expression Atlas closed?
RNA-Seq cell-line
updated 3 days ago by • 0 • written 5.9 years ago by ★ 1.7k
121,094 results • Page 1 of 2422
Recent Votes
What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
Answer: Best choices for DGE and pathway enrichment analysis in single cell data using p
Comment: How to generate identiy score between aligned sequences with Mauve?
Remove sequences <300 bases from FASTA file
Answer: Bioinformatics Docker Images Project (https://pegi3s.github.io/dockerfiles/)
Single cell RNA-seq analysis
Single cell RNA-seq analysis
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Comment: Create local Blast database alias with blastdb_aliastool fails by etienne • 0
Thank you. How do you checked the GI with the N/A response? Is there a way to alias using accession numbers? Or taxID? I need to make a da…
Comment: Best choices for DGE and pathway enrichment analysis in single cell data using p by txema.heredia ▴ 210
Thank you for your insights! Yes, I also lack formal stats education. I tend to use simple tests because they are easier to interpret (bot…
Answer: How can I find KO IDs for ORF sequences in a large FASTA file? by Mensur Dlakic ★ 29k
There is a tool made exactly for that purpose: https://github.com/takaram/kofam_scan
Answer: Normalization - Tissue specificity analysis by Pallavi • 0
They develop TransTEx to look at Tissue specific transcripts. Check out their database. [TransTEx][1] [1]: https://academic.oup.c…
Answer: Transcript Specific Expression Data by Pallavi • 0
We developed TransTEx to look at Tissue specific transcripts [TransTEx][1] [1]: https://academic.oup.com/bioinformatics/article/40/8/…
Answer: Database To Look For Tissue-Specific Transcript Expression Of The Same Gene. by Pallavi • 0
We developed TransTEx to look at Tissud specific transcripts [TransTEx][1] [1]: https://academic.oup.com/bioinformatics/article/…
Comment: Featurecounts: Unexpected number of features by JourneyToAbyss ▴ 240
I have played around with salmon. However, featurecounts appears more transparant in where the information, from the gtf file, is coming fr…
Comment: Featurecounts: Unexpected number of features by GenoMax 151k
Have you considered using `salmon` or `kallisto`?
Comment: Sequence length from Fasta by Diogenes • 0
This is pretty good. Exactly what I was looking for. Works very well in command line, and they have conda installation, so easy installtio…
Comment: Interpreting a vcf file by cmdcolin ★ 4.2k
this is a pretty weird VCF file as there is no "GT" field
Comment: Bioinformatics Docker Images Project (https://pegi3s.github.io/dockerfiles/) by Jeremy Leipzig 23k
anyone who is using Chrome will see "bdip.i3s.up.pt doesn’t support a secure connection" and will assume this is some sketchy scam you sho…
Answer: Bioinformatics Docker Images Project (https://pegi3s.github.io/dockerfiles/) by Hugo ▴ 400
Dear colleagues, Since the creation of the project, it has been growing constantly and we have recently created a new website: http://bdip…
Comment: Featurecounts: Unexpected number of features by JourneyToAbyss ▴ 240
Transcriptional level is something I am interested in and why I am looking at this at a finer detail.
Comment: Featurecounts: Unexpected number of features by JourneyToAbyss ▴ 240
Yes there is. I am trying to replicate previous results before updating it.
Comment: How to generate identiy score between aligned sequences with Mauve? by GenoMax 151k
Looks like a file header is required for the `csv` file (as below). Try this file. sample,fasta HoVa25_chr1,chr1_out.fa Query_…
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