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120,386 results • Page
1 of 2408
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40
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Pipelines/Tools for cleaning UK Biobank data?
UKBiobank
RAP
4 hours ago by
Christian
• 0
0
votes
0
replies
34
views
GO Analysis Combine or Separate DEGs
clusterProfiler
GO
4 hours ago by
Koki
• 0
828
votes
169
replies
166k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
3.4k • written 8.2 years ago by
Istvan Albert
102k
0
votes
0
replies
38
views
Key error when using prepDE.py
python
prepDE
stringtie
keyerror
5 hours ago by
mohamadelian1996
• 0
0
votes
2
replies
88
views
How to use harmony with scanpy?
scanpy
harmony
3 hours ago by
bioinfo
▴ 150
0
votes
2
replies
92
views
Scdblfinder issue
R
scdblfinder
updated 2 hours ago by
Ram
44k • written 7 hours ago by
rahma.khoualdia
• 0
0
votes
0
replies
47
views
Repeat Modeler Database Generation
repeat_modeler
repeats
fungi
annotation
genomes
7 hours ago by
SomeOne
▴ 170
0
votes
2
replies
95
views
Merging paired-end reads after featureCounts
featureCounts
RNAseq
updated 6 hours ago by
ATpoint
86k • written 8 hours ago by
n_navy
• 0
0
votes
1
reply
78
views
Proteomics DEA
Proteomics
updated 6 hours ago by
ATpoint
86k • written 8 hours ago by
frarodmar17
• 0
0
votes
0
replies
45
views
Difficulty Finding LRR SD and BAF Drift in GenomeStudio 2.0
array
LRR
BAF
genomestudio
snp
9 hours ago by
Josephine H.
• 0
3
votes
5
replies
153
views
ATAC-seq paired-end data peakcalling on MACS3 - BAMPE vs (BAM and shift with extsize)
MACS3
BAMPE
BAM
Peakcalling
ATAC-seq
updated 6 hours ago by
ATpoint
86k • written 10 hours ago by
Manko47
▴ 10
0
votes
1
reply
79
views
LH Sequencing Machine?
fastq
updated 8 hours ago by
GenoMax
149k • written 10 hours ago by
andrebolerbarros
• 0
5
votes
5
replies
242
views
6 follow
High memory sorting of kmers - best way to use sort
uniq
linux
sort
kmers
updated 7 hours ago by
Ram
44k • written 23 hours ago by
r.ackbersingh
▴ 30
0
votes
0
replies
55
views
News:
Bayesian Data Analysis in R – Online Course (March 3-7)
R
RegressionModeling
Statistics
Byesian
14 hours ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
74
views
Age covariate in GWAS
GWAS
14 hours ago by
aaaniich
• 0
2
votes
4
replies
570
views
How to completely align chromosomes/scaffolds from de novo genome assemblies using MUMMER or other tools?
visualization
genome
alignment
updated 14 hours ago by
christophe.klopp
▴ 20 • written 6 days ago by
Drew
• 0
5
votes
8
replies
469
views
How well was the rRNA depletion for RNA-Seq experiments
contamination
star
rrna
bbduk
ribodetector
updated 8 hours ago by
GenoMax
149k • written 12 days ago by
gogeni5529
▴ 60
0
votes
0
replies
69
views
News:
Introduction to Machine Learning with R - online, March 3–7
R
Machine-Learning
omics
Genomics
updated 6 hours ago by
Ram
44k • written 16 hours ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
91
views
Job:
2025 Summer Internship Opportunity in Computational Biology
intern
18 hours ago by
Shicheng Guo
★ 9.6k
2
votes
5
replies
1.3k
views
Tools for fasterq file?
trimming
updated 18 hours ago by
AB
▴ 370 • written 2.3 years ago by
shinyjj
▴ 50
3
votes
9
replies
1.7k
views
How to convert fasterq File into fastq files ?
fastq
fasterq
updated 19 hours ago by
AB
▴ 370 • written 2.2 years ago by
NikhilP
▴ 20
2
votes
5
replies
175
views
How to extract DEGs from GEO database
extract
DEGs
12 hours ago by
harrydo1892
• 0
0
votes
1
reply
126
views
plotProfile Errors of DiffBind
DiffBind
updated 17 hours ago by
GenoMax
149k • written 1 day ago by
lijiangres
• 0
10
votes
5
replies
262
views
In silico prediction if a phage can invade a bacterium
phage
bacterium
11 hours ago by
A_heath
▴ 170
0
votes
4
replies
3.5k
views
BEAST and BEAGLE installed using conda environment, how to connect?
BEAST
BEAUTI
updated 22 hours ago by
sbrobeson
• 0 • written 5.1 years ago by
kabir.deb
▴ 90
1
vote
3
replies
237
views
Dimensionality reduction using RNA and protein expression
dimensionality-reduction
RNA-seq
spatial
updated 1 day ago by
LChart
4.8k • written 2 days ago by
noodlejackson
▴ 20
5
votes
2
replies
554
views
java out of memory error through beagle for imputation
beagle
imputation
java
updated 1 day ago by
Ram
44k • written 9 months ago by
analyst
▴ 60
0
votes
2
replies
333
views
BioPython load/save from SnapGene
biopython
1 day ago by
tada
• 0
1
vote
1
reply
149
views
Herald:
The Biostar Herald for Monday, February 10, 2025
herald
updated 1 day ago by
Bastien Hervé
6.1k • written 1 day ago by
Biostar
3.4k
1
vote
1
reply
232
views
Get bond angles for nucleotides in pdb/cif structure file
cif
cryoEM
pymol
pdb
structure
updated 1 day ago by
dthorbur
★ 2.7k • written 4 days ago by
noodle
▴ 640
4
votes
7
replies
255
views
merging .fastq.gz files results in corrupted files
corrupt
gzip
9 hours ago by
rDNA
▴ 20
0
votes
1
reply
127
views
Installing VEP for a Specific Chromosome (e.g., Chromosome 1) is not possible??
VEP
updated 1 day ago by
dthorbur
★ 2.7k • written 1 day ago by
Manuel
▴ 50
0
votes
3
replies
174
views
Blast+ remote search for refseq reference genome
API
refseq
updated 16 hours ago by
GenoMax
149k • written 1 day ago by
Chiranth
• 0
0
votes
1
reply
168
views
Finding target for the biologically active compound
target-prediction
updated 1 day ago by
dthorbur
★ 2.7k • written 2 days ago by
Pragya
• 0
0
votes
3
replies
188
views
single-cell transcriptomics and bulk proteomics data integration
integration
omics
data
updated 1 day ago by
AB
▴ 370 • written 1 day ago by
frarodmar17
• 0
1
vote
2
replies
166
views
Split genotypes in VCF file
VCF
genotype
dipcall
1 day ago by
Biomonika (Noolean)
3.2k
0
votes
2
replies
136
views
clinker, a gene cluster visualization tool, crashed its online site
cluster
gene
updated 1 day ago by
ATpoint
86k • written 1 day ago by
yinfang
• 0
4
votes
2
replies
302
views
Using limma on a very low ammount of genes
DE-Analysis
limma
updated 1 day ago by
Gordon Smyth
★ 7.8k • written 9 days ago by
ijarne
▴ 20
2
votes
2
replies
243
views
Snakemake version 8.27.1 on LSF cluster
metagenomics
snakemake
shotgun
kraken2
updated 1 day ago by
DBScan
▴ 470 • written 3 days ago by
John
• 0
5
votes
3
replies
188
views
Bcftools extracting list of markers by chr and pos
bcftools
updated 1 day ago by
Ram
44k • written 1 day ago by
am29
▴ 60
1
vote
1
reply
176
views
differential gene expression in male and female samples
CLCworkbench
RNAseq
updated 2 days ago by
ATpoint
86k • written 2 days ago by
BioS
• 0
0
votes
0
replies
125
views
News:
Online Course: Machine Learning Methods for Longitudinal Data with Python
Longitudinal-Data
Machine-Learning
Deep-Learning
Omics
updated 1 day ago by
Ram
44k • written 2 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
209
views
Issue with Converting Excel Data to JSON
python
classifier
json
machine-learning
updated 2 days ago by
natasha.sernova
★ 4.0k • written 3 days ago by
Cake Day
• 0
4
votes
4
replies
319
views
Nanopore DRS data
m6A
PolyA-tail
DRS
Nanopore
updated 6 hours ago by
GenoMax
149k • written 4 days ago by
baibhu1234
▴ 20
0
votes
1
reply
227
views
Figures and plots for integration of ATAC and RNA seq data
ATAC-seq
RNA-seq
updated 2 days ago by
jared.andrews07
★ 18k • written 3 days ago by
SpartanII
• 0
1
vote
1
reply
171
views
Issue with picard index in my one chr reference fasta file
SamToFastq
1 day ago by
Manuel
▴ 50
0
votes
0
replies
163
views
News:
course: Generalised Linear Models in R - Online, 24–28 February.
R
Generalised-Linear-Models
GLM
updated 1 day ago by
Ram
44k • written 3 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
174
views
News:
Seafood Genomics course - Online, February 25-28
qPCR
Genomic-Traceability
Nanopore
Seafood-Genomics
updated 1 hour ago by
Jeremy Leipzig
23k • written 3 days ago by
Physalia-courses
★ 2.6k
0
votes
8
replies
360
views
Bowtie2 keeps exiting with "Error reading _plen[] array:"
bowtie2
updated 3 days ago by
GenoMax
149k • written 3 days ago by
biobaker
• 0
1
vote
2
replies
313
views
How to Generate tissue_lowres_image.png from tissue_hires_image.png for spatial transcriptomics?
seurat
spatial-transcriptomics
updated 1 day ago by
Ram
44k • written 3 days ago by
Ibrahim
• 0
120,386 results • Page
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Recent Votes
The Biostar Handbook. A bioinformatics e-book for beginners.
Answer: ATAC-seq paired-end data peakcalling on MACS3 - BAMPE vs (BAM and shift with ext
Answer: ATAC-seq paired-end data peakcalling on MACS3 - BAMPE vs (BAM and shift with ext
Answer: ATAC-seq paired-end data peakcalling on MACS3 - BAMPE vs (BAM and shift with ext
Answer: Transform a GTF file into a data frame in R
Answer: Transform a GTF file into a data frame in R
Answer: How to choose cells that co-express several genes with scanpy?
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Comment: Whether personalized pangenome considers allele frequency
by
Wang Cong
▴ 20
Thanks! For diploid sampling mode, does the hap1 has the highest score and hap2 has the second highest score?
Comment: Seafood Genomics course - Online, February 25-28
by
Jeremy Leipzig
23k
sounds like a great oppor-tuna-ty. you guys are krilling it!
Comment: Unable to get to BAM file from SAM using samtools
by
GenoMax
149k
That is a confusing way to provide input options (am not a `cutadapt` user) but you are right. I will scratch my comment above. At this po…
Comment: Unable to get to BAM file from SAM using samtools
by
alejandro.mejiam1
▴ 20
I´ve actually done this with other samples and with some of them the actual SAM to BAM step can be done. Additionally, I looked for it in …
Comment: How to use harmony with scanpy?
by
bioinfo
▴ 150
Thank you for your reply. After running Harmony I do the below: adata.obsm['X_pca'] = adata.obsm['X_pca_harmony'] sc.pp.neighbors(…
Answer: How to use harmony with scanpy?
by
LChart
4.8k
Harmony performs batch effect correction on an embedding space, `.obsm['X_pca']` by default, but you can change this by passing `basis=`. I…
Comment: Merging paired-end reads after featureCounts
by
ATpoint
86k
What is "from 3 people"? Please try to use some sort of more professional lingo.
Comment: ATAC-seq paired-end data peakcalling on MACS3 - BAMPE vs (BAM and shift with ext
by
ATpoint
86k
Oh, it's part of macs now. I was referring to the standalone version from their paper. Ok, maybe try it then, they might have made notable …
Answer: Scdblfinder issue
by
jared.andrews07
★ 18k
You should read about [how to ask a good question](https://www.biostars.org/p/75548/), as your post provides zero context or even what you'…
Comment: ATAC-seq paired-end data peakcalling on MACS3 - BAMPE vs (BAM and shift with ext
by
jared.andrews07
★ 18k
Huh, good to know. I never even realized it was a command until recently.
Comment: ATAC-seq paired-end data peakcalling on MACS3 - BAMPE vs (BAM and shift with ext
by
ATpoint
86k
...and it will take hours last time I tried. Given there hasn't been a GitHub commit in 6 years it might still be that slow.
Comment: Scdblfinder issue
by
Ram
44k
This is not a good way to ask a question. Please see the guideline post: https://www.biostars.org/p/179963/
Comment: Proteomics DEA
by
ATpoint
86k
limma is a specific differential expression analysis --in my opinion the most generic and useful one for most HT datasets.
Comment: High memory sorting of kmers - best way to use sort
by
Ram
44k
Please do not use `bioinformatics` as a tag unless your post is about the field of bioinformatics itself. For proper examples, please see F…
Comment: ATAC-seq paired-end data peakcalling on MACS3 - BAMPE vs (BAM and shift with ext
by
jared.andrews07
★ 18k
You might also try MACS3's [hmmratac](https://macs3-project.github.io/MACS/docs/hmmratac.html) tool. I haven't given it a try, but it may b…
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