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121,341 results • Page
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13
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single-cell differential expression of unbalanced cell number
Seurat
scRNA-seq
1 hour ago by
Yingying
▴ 10
0
votes
1
reply
509
views
Differential Expression tests for cell-type clusters from a single-cell RNAseq dataset with no biological replicates
cell-type
DEG
DE
single-cell
updated 1 hour ago by
Yingying
▴ 10 • written 5 months ago by
aa23871x
• 0
0
votes
2
replies
48
views
Annotation Issue using miRBASE gff
NGS
miRNA
1 hour ago by
anthony.santana.703.j
▴ 30
0
votes
0
replies
43
views
News:
Evo 2 webinar - 1 day left to register
AI.LLM.Biology.Genomics
6 hours ago by
Claire Watson
▴ 60
839
votes
170
replies
179k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 6 weeks ago by
Biostar
3.6k • written 8.5 years ago by
Istvan Albert
102k
1
vote
2
replies
83
views
Error Scaffolding with RagTag
scaffold
RagTag
updated 3 hours ago by
GenoMax
151k • written 7 hours ago by
Bipin
▴ 10
0
votes
2
replies
97
views
Identify transgene insert loci/copy number in nanopore De-novo assembly
ont
nanopore
transgene
sequencing
wgs
6 hours ago by
ctmfarland
• 0
2
votes
0
replies
60
views
Tool:
biothings-mcp - MCP server to query genes, variants, chemicals, taxons
API
biothings
genes
AI
MCP
7 hours ago by
Anton
▴ 80
2
votes
0
replies
54
views
Tool:
synergy-age-mcp - a database of synergistic and antagonistic genetic interactions in longevity
combination
longevity
MCP
ageing
10 hours ago by
Anton
▴ 80
2
votes
0
replies
55
views
Tool:
opengenes-mcp - MCP server on the database for longevity genes
genes
databases
bioinformatics
longevity
MCP
10 hours ago by
Anton
▴ 80
2
votes
0
replies
62
views
Tool:
gget-mcp - a bioinformatics toolkit for genomics queries and analysis (based on gget lbrary)
bioinformatics
libraries
MCP
AI
10 hours ago by
Anton
▴ 80
0
votes
2
replies
99
views
Best pairwise alignment for insertion and deletion-containing sequences
sequence
python
biopython
pairwise
alignment
11 hours ago by
rbpdee
▴ 50
0
votes
2
replies
116
views
Heatmap for visualizing the differentially expressed genes in RNA-seq data
R
DEseq2
RNA-seq
differentially-expressed
heatmap
updated 4 hours ago by
rfran010
★ 1.5k • written 12 hours ago by
KABILAN
▴ 130
0
votes
7
replies
252
views
How to deal with intermediate files
procedures
data
operations
updated 8 hours ago by
GenoMax
151k • written 1 day ago by
ramiro.barrantes
▴ 50
1
vote
1
reply
93
views
Quality control metrics in mmCIF
PDB
protein
mmCIF
updated 13 hours ago by
dthorbur
★ 3.0k • written 16 hours ago by
Adrian
• 0
0
votes
1
reply
90
views
phage sequence no alignment to genome
prophage
bwa
phage
genome
alignment
updated 12 hours ago by
GenoMax
151k • written 14 hours ago by
Luwell
• 0
0
votes
1
reply
87
views
Mitochondrial Annotation Tool
Illumina
Bovine
Mitochondria
updated 14 hours ago by
patrickdm
▴ 260 • written 15 hours ago by
adarsh
▴ 60
1
vote
1
reply
134
views
Assessing the difference between a de novo assembly and a reference genome
hifiasm
MUMmmer
dnadiff
updated 16 hours ago by
patrickdm
▴ 260 • written 1 day ago by
andrea
• 0
0
votes
1
reply
98
views
HISAT2 or STAR
alignment
hisat2
star
updated 4 hours ago by
rfran010
★ 1.5k • written 18 hours ago by
Shazel
• 0
0
votes
2
replies
113
views
What to do after fastp?
rna-seq
fastp
alignment
updated 14 hours ago by
dthorbur
★ 3.0k • written 18 hours ago by
Shazel
• 0
1
vote
1
reply
251
views
SNP calling from multiple genomes: No valid SNPs
samtools
bcftools
snp
plink
wgs
updated 1 day ago by
colindaven
7.6k • written 4 days ago by
emil.paulitz
• 0
0
votes
0
replies
96
views
ATAC-seq analysis
atac-seq
hmmratac
calling
peak
macs3
updated 1 day ago by
GenoMax
151k • written 1 day ago by
SEJAL
• 0
0
votes
1
reply
143
views
Bioconductor scRNAseq tutorial constantly breaks down due to dependencies
R
Bioconductor
scRNAseq
RNAseq
updated 1 day ago by
GenoMax
151k • written 1 day ago by
bn
▴ 30
0
votes
0
replies
140
views
Trouble building combined pangenome graph with circularized genomes + embedded ORF1 paths
vg
updated 2 days ago by
GenoMax
151k • written 2 days ago by
Floren
• 0
0
votes
1
reply
477
views
HOMER findMotifsGenome.pl failed compilation
findMotifsGenome.pl
motifanalysis
HOMER
updated 2 days ago by
文杰
• 0 • written 3 months ago by
India
• 0
0
votes
0
replies
147
views
News:
Introduction to Genome-Wide Association Studies (GWAS) | 23-27 June
StatisticalPower
GWAS
Imputation
2 days ago by
Physalia-courses
★ 2.6k
0
votes
4
replies
2.0k
views
normalize between 2 different platform
RNA-Seq
updated 2 days ago by
linqy
▴ 10 • written 8.4 years ago by
Edalat
▴ 30
1
vote
0
replies
148
views
How to normalize bulk TCR-seq data generated by different methods and platforms
TCR
bioinformatics
analysis
3 days ago by
linqy
▴ 10
0
votes
1
reply
213
views
Building database with snpEff -- -gtf22 option not recognized/file not read
snpeff
updated 3 days ago by
GenoMax
151k • written 3 days ago by
michael.dhar
• 0
2
votes
4
replies
902
views
Discussions about QC of sc-multiomic-ATAC_RNA-seq from 10xgenomics platform in terms of using repetitive elements to filter peaks
sequence
scatac
cell
single
10xatac
3 days ago by
gynecoloji
• 0
0
votes
2
replies
285
views
Using VEP custom input
gnomAD
constraint
LOEUF
VEP
pLI
3 days ago by
Sd
• 0
0
votes
0
replies
180
views
Bacterial transcriptome analysis- any need for --dta in HISAT2?
dta
stringtie
transcriptome
bacterial
hisat2
3 days ago by
a58c4637
• 0
8
votes
5
replies
398
views
nanopore unaligned bam files
nanopore
updated 3 days ago by
GenoMax
151k • written 3 days ago by
sarahmanderni
▴ 130
0
votes
0
replies
174
views
I woudl ike to understnad how to set the aucMaxRank value for my data set
AUCell
aucMaxRank
3 days ago by
gogeni5529
▴ 70
0
votes
1
reply
237
views
Issue with Package installation in R.
R
GCC
updated 3 days ago by
GenoMax
151k • written 3 days ago by
harsh
▴ 20
0
votes
0
replies
168
views
MAPQ algorithms of Giraffe
giraffe
vg
3 days ago by
gulin
• 0
5
votes
4
replies
649
views
Phased haplotype using WGS data from Nebula Genomics and GATK
phased
nebula
haplotype
wgs
gatk
updated 3 days ago by
colindaven
7.6k • written 12 days ago by
biostars
▴ 30
0
votes
1
reply
218
views
IGV view for Chromatin accessibility ATAC-seq
ATAC-seq
updated 3 days ago by
ATpoint
88k • written 4 days ago by
Vxike
• 0
2
votes
2
replies
1.8k
views
How to interpret Nucleosome banding pattern in scATAC-Seq?
single-cell
scATAC-Seq
Signac
transcriptomics
updated 4 days ago by
Jan
• 0 • written 3.6 years ago by
patelk26
▴ 340
4
votes
2
replies
287
views
WGCNA blockwiseModules function for small datasets
WGCNA
blockwiseModules
3 days ago by
ATS
▴ 10
1
vote
4
replies
305
views
How to add GFP in STAR reference?
STAR
updated 4 days ago by
GenoMax
151k • written 4 days ago by
bioinfo
▴ 160
0
votes
0
replies
191
views
News:
Population Genomics Using Ancient DNA Data course
DemographicModels
PopulationGenomics
aDNA
Genomics
4 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
234
views
Can you compare GETx and TCGA miRNA non normalized counts a
comapre
to
how
updated 4 days ago by
ATpoint
88k • written 4 days ago by
radwa_noreen
• 0
0
votes
3
replies
350
views
ATAC-seq analysis
ATAC-seq
Samtools
Sorting
updated 4 days ago by
ATpoint
88k • written 5 days ago by
SEJAL
• 0
0
votes
1
reply
264
views
Learn tNGS
tNGS
updated 4 days ago by
GenoMax
151k • written 4 days ago by
hang
• 0
4
votes
3
replies
407
views
Server Requirements for long read data analysis
longreadserver
longreadanalysis
serverrequirements
Server
updated 4 days ago by
colindaven
7.6k • written 5 days ago by
genomics_student
• 0
0
votes
1
reply
266
views
The molecular signatures database (MSigDB) in R
MSigDB
updated 4 days ago by
marco.barr
▴ 170 • written 4 days ago by
Kelly
• 0
2
votes
3
replies
653
views
plotProfile Errors of DiffBind
DiffBind
4 days ago by
lijiangres
▴ 20
0
votes
0
replies
236
views
Job:
Lab Head positions at the WEHI, Melbourne Australia
LabHead
Australia
JobPosting
4 days ago by
Gordon Smyth
★ 8.1k
0
votes
0
replies
221
views
Merging single ATAC seq data sets from multiple sample
10x
5 days ago by
1769mkc
★ 1.3k
121,341 results • Page
1 of 2427
Recent Votes
For CreateSeuratObject, Where Do the Values for min.cells and min.features come from?
Error Scaffolding with RagTag
C: The Biostar Handbook. A bioinformatics e-book for beginners.
Filter out doublet and Clustering
How to adjust for homotypic doublets in the R package DoubletFinder
C: Remove Extra Info From Fasta Header
Remove Extra Info From Fasta Header
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Recent Replies
Answer: Differential Expression tests for cell-type clusters from a single-cell RNAseq d
by
Yingying
▴ 10
Hi, just wanted to ask if you've got any answers?
Comment: Annotation Issue using miRBASE gff
by
anthony.santana.703.j
▴ 30
As awlays Geno, thank you so much for helping, although I thought the same thing, I looked online the according to everything the gff from …
Comment: Annotation Issue using miRBASE gff
by
GenoMax
151k
You can't mix and match genome sequence and annotations. If you used a prebuilt bowtie index from NCBI then you will need to find an annota…
Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
by
rfran010
★ 1.5k
Generally, fold-changes can be hard to distinguish from TPMs between samples when TPM variability between genes is large. Gene-wise scaling…
Comment: HISAT2 or STAR
by
rfran010
★ 1.5k
Generally, they are equivalent. They both are designed to handle spliced reads (e.g. RNA-seq) well. HISAT2 may be better if you are on a m…
Comment: Error Scaffolding with RagTag
by
Bipin
▴ 10
[M::mm_idx_gen::73.687*1.32] collected minimizers [M::mm_idx_gen::75.834*1.84] sorted minimizers [M::main::75.834*1.84] loaded/…
Comment: Identify transgene insert loci/copy number in nanopore De-novo assembly
by
ctmfarland
• 0
Thanks for the prompt response! * min: 67, max: 93,862, avg: 3,626, q25: 2737, q75: 4406 * minION * 1,150,160 reads total/used and calcula…
Comment: Error Scaffolding with RagTag
by
GenoMax
151k
Is there anything in `ragtag.scaffold.asm.paf.log` file?
Comment: Identify transgene insert loci/copy number in nanopore De-novo assembly
by
GenoMax
151k
> the average read length in my ONT library is ~3Kbp What is the range of read lengths in this dataset? Was this run on a minION or larger…
Comment: How to deal with intermediate files
by
GenoMax
151k
Not sure I fully understand your question. Many of us use the local computer as a dumb terminal to get to the HPC where much of the work ha…
Comment: How to deal with intermediate files
by
ramiro.barrantes
▴ 50
Yes, from my laptop I do the final reports with graphs, etc and all the code is source controlled with git. I am not computing anything on …
Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
by
jared.andrews07
★ 18k
Show example images and the code used to generate them. We can't see what you see, so it's hard to say if you are plotting things incorrect…
Comment: How to deal with intermediate files
by
GenoMax
151k
> One simpler way that is closer is for example to mount the locations on our HPC to my laptop and hence not having to transfer anything A…
Comment: How to deal with intermediate files
by
ramiro.barrantes
▴ 50
Thank you!! I am aware of all of those, however, they are not exactly what I am looking for: I could transfer data from one place to anothe…
Comment: Best pairwise alignment for insertion and deletion-containing sequences
by
rbpdee
▴ 50
Thanks, @patrickdm! Let me give it a shot.
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