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121,346 results • Page
1 of 2427
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11
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Signature Matrix Modifications/Subclustering
signature
matrix
scRNA-seq
seurat
cibersortx
41 minutes ago by
MitchT
• 0
0
votes
0
replies
10
views
Does Beagle use the reference genome for both phasing AND imputing genotypes?
beagle
genotypes
phasing
imputation
43 minutes ago by
giulia.trauzzi
▴ 30
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
0
votes
0
replies
12
views
In GERPplusplus, odd gerpelem outputs
GERP
evolutionary
gerpcol
substitution
gerpelem
rates
rejected
57 minutes ago by
Begonia_pavonina
▴ 210
0
votes
0
replies
17
views
Time scaled tree with IQTree giving off looking branch length
bacteria
phylogeny
time
evolution
scaled
1 hour ago by
SushiRoll
▴ 140
1
vote
1
reply
47
views
required annotations for VQSR
VQSR
vcf
annotation
updated 2 hours ago by
BEST
• 0 • written 3 hours ago by
Mahdi&Christ
▴ 10
0
votes
3
replies
146
views
Identify transgene insert loci/copy number in nanopore De-novo assembly
ont
nanopore
transgene
sequencing
wgs
updated 2 hours ago by
colindaven
7.6k • written 19 hours ago by
ctmfarland
• 0
6
votes
7
replies
246
views
Heatmap for visualizing the differentially expressed genes in RNA-seq data
R
DEseq2
RNA-seq
differentially-expressed
heatmap
1 hour ago by
KABILAN
▴ 130
0
votes
1
reply
88
views
single-cell differential expression of unbalanced cell number
Seurat
scRNA-seq
updated 5 hours ago by
ATpoint
88k • written 12 hours ago by
Yingying
▴ 10
0
votes
1
reply
578
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 13 hours ago by
Yingying
▴ 10 • written 5 months ago by
aa23871x
• 0
1
vote
5
replies
172
views
Annotation Issue using miRBASE gff
NGS
miRNA
updated 30 minutes ago by
GenoMax
151k • written 13 hours ago by
anthony.santana.703.j
▴ 30
0
votes
0
replies
72
views
News:
Evo 2 webinar - 1 day left to register
AI.LLM.Biology.Genomics
18 hours ago by
Claire Watson
▴ 60
1
vote
3
replies
132
views
Error Scaffolding with RagTag
scaffold
RagTag
updated 20 minutes ago by
GenoMax
151k • written 19 hours ago by
Bipin
▴ 10
2
votes
0
replies
85
views
Tool:
biothings-mcp - MCP server to query genes, variants, chemicals, taxons
API
biothings
genes
AI
MCP
19 hours ago by
Anton
▴ 80
2
votes
0
replies
76
views
Tool:
synergy-age-mcp - a database of synergistic and antagonistic genetic interactions in longevity
combination
longevity
MCP
ageing
22 hours ago by
Anton
▴ 80
2
votes
0
replies
76
views
Tool:
opengenes-mcp - MCP server on the database for longevity genes
genes
databases
bioinformatics
longevity
MCP
22 hours ago by
Anton
▴ 80
2
votes
0
replies
91
views
Tool:
gget-mcp - a bioinformatics toolkit for genomics queries and analysis (based on gget lbrary)
bioinformatics
libraries
MCP
AI
22 hours ago by
Anton
▴ 80
0
votes
2
replies
125
views
Best pairwise alignment for insertion and deletion-containing sequences
sequence
python
biopython
pairwise
alignment
22 hours ago by
rbpdee
▴ 50
1
vote
7
replies
289
views
How to deal with intermediate files
procedures
data
operations
updated 19 hours ago by
GenoMax
151k • written 1 day ago by
ramiro.barrantes
▴ 60
1
vote
1
reply
111
views
Quality control metrics in mmCIF
PDB
protein
mmCIF
updated 1 day ago by
dthorbur
★ 3.0k • written 1 day ago by
Adrian
• 0
0
votes
1
reply
107
views
phage sequence no alignment to genome
prophage
bwa
phage
genome
alignment
updated 1 day ago by
GenoMax
151k • written 1 day ago by
Luwell
• 0
0
votes
1
reply
108
views
Mitochondrial Annotation Tool
Illumina
Bovine
Mitochondria
updated 1 day ago by
patrickdm
▴ 260 • written 1 day ago by
adarsh
▴ 60
1
vote
1
reply
155
views
Assessing the difference between a de novo assembly and a reference genome
hifiasm
MUMmmer
dnadiff
updated 1 day ago by
patrickdm
▴ 260 • written 1 day ago by
andrea
• 0
0
votes
1
reply
129
views
HISAT2 or STAR
alignment
hisat2
star
updated 16 hours ago by
rfran010
★ 1.5k • written 1 day ago by
Shazel
• 0
0
votes
2
replies
133
views
What to do after fastp?
rna-seq
fastp
alignment
updated 1 day ago by
dthorbur
★ 3.0k • written 1 day ago by
Shazel
• 0
1
vote
1
reply
272
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
115
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
163
views
Bioconductor scRNAseq tutorial constantly breaks down due to dependencies
R
Bioconductor
scRNAseq
RNAseq
updated 2 days ago by
GenoMax
151k • written 2 days ago by
bn
▴ 30
0
votes
0
replies
158
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
494
views
HOMER findMotifsGenome.pl failed compilation
findMotifsGenome.pl
motifanalysis
HOMER
updated 3 days ago by
文杰
• 0 • written 3 months ago by
India
• 0
0
votes
0
replies
163
views
News:
Introduction to Genome-Wide Association Studies (GWAS) | 23-27 June
StatisticalPower
GWAS
Imputation
3 days ago by
Physalia-courses
★ 2.6k
0
votes
4
replies
2.1k
views
normalize between 2 different platform
RNA-Seq
updated 3 days ago by
linqy
▴ 10 • written 8.4 years ago by
Edalat
▴ 30
1
vote
0
replies
166
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
232
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
1.0k
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
306
views
Using VEP custom input
gnomAD
constraint
LOEUF
VEP
pLI
3 days ago by
Sd
• 0
0
votes
0
replies
195
views
Bacterial transcriptome analysis- any need for --dta in HISAT2?
dta
stringtie
transcriptome
bacterial
hisat2
4 days ago by
a58c4637
• 0
8
votes
5
replies
429
views
nanopore unaligned bam files
nanopore
updated 3 days ago by
GenoMax
151k • written 4 days ago by
sarahmanderni
▴ 130
0
votes
0
replies
196
views
I woudl ike to understnad how to set the aucMaxRank value for my data set
AUCell
aucMaxRank
4 days ago by
gogeni5529
▴ 70
0
votes
1
reply
252
views
Issue with Package installation in R.
R
GCC
updated 3 days ago by
GenoMax
151k • written 4 days ago by
harsh
▴ 20
0
votes
0
replies
186
views
MAPQ algorithms of Giraffe
giraffe
vg
4 days ago by
gulin
• 0
5
votes
4
replies
668
views
Phased haplotype using WGS data from Nebula Genomics and GATK
phased
nebula
haplotype
wgs
gatk
updated 4 days ago by
colindaven
7.6k • written 12 days ago by
biostars
▴ 30
0
votes
1
reply
234
views
IGV view for Chromatin accessibility ATAC-seq
ATAC-seq
updated 4 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
308
views
WGCNA blockwiseModules function for small datasets
WGCNA
blockwiseModules
3 days ago by
ATS
▴ 10
1
vote
4
replies
324
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
208
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
250
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
370
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
282
views
Learn tNGS
tNGS
updated 5 days ago by
GenoMax
151k • written 5 days ago by
hang
• 0
121,346 results • Page
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Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
Answer: Heatmap for visualizing the differentially expressed genes in RNA-seq data
Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
required annotations for VQSR
Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
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Recent Replies
Comment: Error Scaffolding with RagTag
by
GenoMax
151k
At least in this file there is no immediate smoking gun here. Does the log for successful `madsen` run look similar? Have you checked the S…
Comment: Annotation Issue using miRBASE gff
by
GenoMax
151k
Can you post the output of samtools view your_alignment.bam | head -8 This should show us the "name" of the chromosome that is in yo…
Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
by
KABILAN
▴ 130
Yeah... you're right. Now I have done according to the post. The code I have used is ``` heat_df_centered <- t(apply(heat_df, 1, function(x…
Answer: required annotations for VQSR
by
BEST
• 0
Hi, you're in a common scenario when working with variants that lack the necessary annotations for Variant Quality Score Recalibration (VQS…
Answer: Identify transgene insert loci/copy number in nanopore De-novo assembly
by
colindaven
7.6k
Interesting, your analysis might be correct. One way forward - grep fastq reads which contain parts of your insert (left side, right…
Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
by
ATpoint
88k
It's not scaled. Scaled means centering data at a mean of zero. Your color code is still 0 to a larger value. Read the manual I posted.
Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
by
KABILAN
▴ 130
Thank you for your comment. I have tried with scaled data and I got the below heatmap. Is it correct? ![enter image description here][1]…
Answer: Heatmap for visualizing the differentially expressed genes in RNA-seq data
by
ATpoint
88k
You have to scale the counts first to emphasize differences. Clustering based on unscaled values emphasizes the magnitude of counts, not di…
Comment: single-cell differential expression of unbalanced cell number
by
ATpoint
88k
In my head 200 is not "little", but obviously the imbalance is big. In such situations I usually do subsampling several times and then see …
Comment: Heatmap for visualizing the differentially expressed genes in RNA-seq data
by
KABILAN
▴ 130
Thank you @rfran010 and @jaredandrews07 for your comments. I have used the DEGs only for my heatmap. The TPM normalized values were calcula…
Comment: Annotation Issue using miRBASE gff
by
anthony.santana.703.j
▴ 30
Hello Geno, You dont understand how much I appreciate you, but yes I used featureCounts my trimming is correct my leniancy on those trim f…
Comment: Mass-spectrometry proteomics
by
Gordon Smyth
★ 8.1k
Your code looks ok (although I can't check the data manipulations that are specific to your own dataset). The DE analysis you have done is …
Comment: Annotation Issue using miRBASE gff
by
GenoMax
151k
> I looked online the according to everything the gff from miRBASE should have been compatible. I looked at the GFF file from miRBase an…
Comment: 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 …
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