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116,824 results • Page
1 of 2337
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Votes
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0
votes
0
replies
9
views
RNA seq analysis
DESeq
RNA-seq
analysis
10 minutes ago by
prifa
• 0
9
votes
3
replies
170
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 57 minutes ago by
b.contreras.moreira
▴ 180 • written 18 hours ago by
ijarne
• 0
0
votes
0
replies
29
views
Chance for trained without experience
bio
updated 36 minutes ago by
ATpoint
82k • written 59 minutes ago by
shehab
• 0
0
votes
0
replies
21
views
How can I analysis Nomalized expression data?
DEseq2
RNA-seq
1 hour ago by
mnx0723
• 0
1
vote
2
replies
62
views
How do I change the title font size in ViolinPlot (Seurat)
Seurat
Violin-Plot
ggplot2
patchwork
1 hour ago by
Assa Yeroslaviz
★ 1.8k
0
votes
0
replies
26
views
Xenium multi sample data
batch
annotation
cell
Xenium
effect
2 hours ago by
Omics data mining
▴ 260
0
votes
2
replies
47
views
Phasing a mixture of two individuals' DNA with long reads
long-reads
phasing
39 minutes ago by
njornet
▴ 20
0
votes
1
reply
56
views
Exploring Diet Effects in Single-Cell RNA Sequencing
batch_effect
scRNA
seurat
integration
updated 2 hours ago by
ATpoint
82k • written 3 hours ago by
Darya
• 0
0
votes
4
replies
73
views
Percentage coverage of reference genome by de novo genome
SAMtools
BWA
alignment
ddRAD
updated 1 hour ago by
Michael
54k • written 3 hours ago by
Lemonhope
• 0
0
votes
0
replies
37
views
Why does my Hi-C contact map show large regions making little to no contact?
BWA-MEM2
Hi-C
PretextMap
3 hours ago by
Winter
• 0
0
votes
4
replies
119
views
A question about reference genome for creating the consensus sequence
fasta
fa
cram
genome
updated 39 minutes ago by
GenoMax
142k • written 10 hours ago by
me
• 0
2
votes
11
replies
2.5k
views
6 follow
CNVKIT - unable to produce scatter and diagram pdfs
cnvkit
updated 4 hours ago by
DGTool
• 0 • written 4.8 years ago by
ww22runner
▴ 60
795
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
0
replies
39
views
Error in plotting PCA plot in seurat
PCA
single-cell
seurat
scRNA
RNA
4 hours ago by
Sumeet
• 0
2
votes
1
reply
52
views
java out of memory error through beagle for imutation
beagle
java.out.of.memory
imputation
5 hours ago by
analyst
▴ 50
0
votes
0
replies
32
views
Generating .bed file and .map file for polyploid vcf file through plink
bed
polyploid
map
plink
6 hours ago by
analyst
▴ 50
0
votes
0
replies
31
views
Blog:
Introduction to The Complete Sequence of a Human Genome
biotech
6 hours ago by
usa.cd.genomics
• 0
0
votes
0
replies
29
views
Blog:
Overview of Nanopore Sequencing
biotech
6 hours ago by
usa.cd.genomics
• 0
0
votes
0
replies
49
views
meffil.snp.concordance
meffil
methylation
snp_concordance
10 hours ago by
kyj222637
• 0
0
votes
0
replies
48
views
PseudobulkExpression.Seurat error
Seurat
pseudo-bulk
11 hours ago by
sooni
▴ 20
1
vote
5
replies
357
views
HCL database download
HCL
updated 10 hours ago by
Ram
43k • written 4 days ago by
sooni
▴ 20
0
votes
1
reply
201
views
barcode of TCR-sequencing
barcode
updated 12 hours ago by
mizraelson
▴ 60 • written 7 days ago by
yueli7
▴ 250
0
votes
2
replies
115
views
STAR aligner error
RNA-seq
STAR
slurm
3 hours ago by
M.
▴ 30
0
votes
0
replies
52
views
monocle 3-- Could not get node in small cluster
monocle3
14 hours ago by
synat.keam
▴ 100
0
votes
1
reply
99
views
Correlating Bulk Differential Expression with quantitative
Differential-Expression
DESeq2
updated 10 hours ago by
Ram
43k • written 15 hours ago by
Nicholas
• 0
1
vote
4
replies
306
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
16 hours ago by
heelpPlease
• 0
0
votes
6
replies
341
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
3 hours ago by
JACKY
▴ 140
0
votes
3
replies
207
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 15 hours ago by
Ram
43k • written 20 hours ago by
schmince
• 0
0
votes
0
replies
75
views
News:
Online course. -Time series analysis and Forecasting in R
Time-Series
Forecasting
R
Stastics
20 hours ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
425
views
HLA-HD tool for genomic imputation
genomics
imputation
bash
updated 14 hours ago by
Javier
• 0 • written 3 months ago by
fra.r.silvestro
▴ 10
0
votes
1
reply
104
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 21 hours ago by
GenoMax
142k • written 21 hours ago by
Sony
▴ 10
5
votes
5
replies
224
views
Error in dimnames(x) <- dn : length of 'dimnames' [2] not equal to array extent
EGSEA
8 hours ago by
Chris
▴ 280
0
votes
1
reply
107
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 23 hours ago by
ATpoint
82k • written 23 hours ago by
ahmad.sajad4541
• 0
1
vote
5
replies
174
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 21 hours ago by
i.sudbery
19k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
127
views
student
epitranscriptomics
updated 1 day ago by
ATpoint
82k • written 1 day ago by
useriwa
• 0
0
votes
0
replies
82
views
Imputation of missing genotypes
panel
beagle
imputation
1 day ago by
analyst
▴ 50
0
votes
3
replies
142
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 21 hours ago by
GenoMax
142k • written 1 day ago by
Assa Yeroslaviz
★ 1.8k
6
votes
1
reply
123
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 1 day ago by
dariober
14k • written 1 day ago by
nhaus
▴ 350
2
votes
2
replies
141
views
Is therer any suggestions on mapping rate of WGBS data?
mapping
read
alignment
WGBS
9 hours ago by
Zeng Jingyu
▴ 60
1
vote
2
replies
223
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 1 day ago by
Weiwen
• 0 • written 2 days ago by
MICOS
▴ 10
0
votes
1
reply
88
views
Correlation Analysis
statistics
methylation
NGS
expression
updated 1 hour ago by
manaswwm
▴ 510 • written 1 day ago by
Researcher
▴ 30
1
vote
2
replies
149
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
19 hours ago by
robert.flynn.21
• 0
1
vote
1
reply
190
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
updated 23 hours ago by
Michael
54k • written 1 day ago by
Guillermo
• 0
1
vote
5
replies
280
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 2 hours ago by
Michael
54k • written 1 day ago by
qwertyuiop26
• 0
0
votes
1
reply
145
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
updated 1 day ago by
ATpoint
82k • written 1 day ago by
MAPK2
▴ 40
0
votes
2
replies
193
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 1 day ago by
Xiaofen
• 0 • written 1 day ago by
toddknutson
▴ 60
0
votes
1
reply
117
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
updated 1 day ago by
LChart
3.9k • written 1 day ago by
David
• 0
1
vote
2
replies
150
views
Where to get the following bed file?
WES
bed
reference
file
updated 1 day ago by
GenoMax
142k • written 1 day ago by
wyuan37
• 0
0
votes
0
replies
96
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
1 day ago by
Scott McKay
▴ 30
0
votes
0
replies
98
views
Cellphonedb results
cpdb
visulization
cellphonedb
1 day ago by
piotto
▴ 20
116,824 results • Page
1 of 2337
Recent Votes
Answer: TFs and Gene databases
Answer: java out of memory error through beagle for imutation
A: Could you explain the difference between STAR, KALLISTO, SALMON etc. to experime
Could you explain the difference between STAR, KALLISTO, SALMON etc. to experimental Biologist/non-bioinformatician
Comment: Microarray pbrobe ID to gene ID problem
Answer: Microarray pbrobe ID to gene ID problem
Answer: How do I change the title font size in ViolinPlot (Seurat)
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Recent Replies
Comment: Soft-clipping read ends based on read group
by
chenl
▴ 10
Hi, Can you please share how did you clip both ends of the reads with ClipReads? Clipping form the start with `-CT "1-3"` for instance wor…
Comment: Phasing a mixture of two individuals' DNA with long reads
by
njornet
▴ 20
This is related to that other question but for now, the only thing I'm interested in is separating the three unique chromosomes, without as…
Comment: A question about reference genome for creating the consensus sequence
by
GenoMax
142k
> I wonder how to adjust the base genome. If you are looking to make changes to the reference you used for alignment then look into http…
Comment: Phasing a mixture of two individuals' DNA with long reads
by
GenoMax
142k
We had a related discussion in a prior thread by OP: https://www.biostars.org/p/9593780/ Do you have genotype (or independent sequence) da…
Answer: TFs and Gene databases
by
b.contreras.moreira
▴ 180
I can also suggest <https://footprintdb.eead.csic.es> which links TFs to their DNA motifs, not their gene targets.
Comment: Correlation Analysis
by
manaswwm
▴ 510
How many methylation and expression values do you have per gene? If per gene you have a table named - *gene_corr*; which has two columns - …
Comment: How do I change the title font size in ViolinPlot (Seurat)
by
Assa Yeroslaviz
★ 1.8k
thx for the explanation. I did look at the function and I also read in the help page, that you get a patchwork object, only when using `co…
Comment: Percentage coverage of reference genome by de novo genome
by
Lemonhope
• 0
Thank you, I'll check out Quast!
Answer: How do I change the title font size in ViolinPlot (Seurat)
by
ATpoint
82k
Looking at the source code of the function it seems that they make individual plots with ggplot when `features` is `> 1` and then use patch…
Comment: Percentage coverage of reference genome by de novo genome
by
Lemonhope
• 0
Thank you for the response to answer you question, no, the ddRADseq data (short paired end illumina reads) for all the samples were used …
Comment: Percentage coverage of reference genome by de novo genome
by
Michael
54k
minimap2 can do this too, mummer (nucmer) is more accurate but slightly slower. If you want to do this as part of generating assembly stati…
Comment: TFs and Gene databases
by
ijarne
• 0
Thank you so much @jaredandrews07 it looks like I will be able to get what I intended with these sources !!
Comment: Percentage coverage of reference genome by de novo genome
by
Joe
21k
If you have contigs for assemblies, using read-based approaches like samtools is probably not the way to go. As you're interested in % cov…
Comment: Exploring Diet Effects in Single-Cell RNA Sequencing
by
ATpoint
82k
Has data been generated in the same batch, so same day, in the same 10x runs?
Answer: Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, C
by
Michael
54k
So I am assuming you have calculated a Burrows-Wheeler transform, then add the FM-index for the first and last column of the BW-matrix. I r…
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