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122,335 results • Page
1 of 2447
Sort: Rank
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Votes
Replies
0
votes
2
replies
102
views
Bioinformatics python
Python
7 hours ago by
ogunjinmirashidat
• 0
2
votes
3
replies
380
views
Exclude from analyzing rna-seq samples
rna-seq
updated 18 hours ago by
Gordon Smyth
★ 8.6k • written 1 day ago by
dropswater
• 0
852
votes
173
replies
222k
views
113 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
handbook
training
updated 10 weeks ago by
Biostar
3.8k • written 9.1 years ago by
Istvan Albert
103k
0
votes
0
replies
57
views
linkage decay for window size
decay
linkage
plink
1 day ago by
296cfd90
• 0
1
vote
1
reply
207
views
Running psiblast on AWS with ElasticBlast
Psiblast
blast
updated 1 day ago by
GenoMax
155k • written 1 day ago by
Joshua
• 0
1
vote
2
replies
381
views
Unable to use rtracklayer import of bigwig files in older chipseq pipeline - work around/alternatives?
bioconductor
rtracklayer
chipseq
LILY
1 day ago by
awsk
• 0
0
votes
0
replies
48
views
degradome data adapter removal
Degradome
FastQC
Adapter
2 days ago by
1000-Logan
• 0
5
votes
5
replies
661
views
Sequencing run and batch variation
RNA
seq
updated 1 day ago by
GenoMax
155k • written 2 days ago by
bioinfo
▴ 160
0
votes
0
replies
100
views
Custom background gene set for enrichment in variant-based analysis?
clusterprofiler
enrichment
pathway
analysis
updated 2 days ago by
newbioinfograd2323
▴ 30 • written 4 days ago by
iamsmor
• 0
0
votes
1
reply
214
views
Why does including BQ<10 bases change Mutect2 calls in NovaSeq X Plus ctDNA data?
novaseq
ctDNA
mutect2
variant-calling
updated 2 days ago by
GenoMax
155k • written 2 days ago by
Anthony
• 0
0
votes
0
replies
70
views
RNA splicing analysis
RNA-seq
Splicing
updated 2 days ago by
GenoMax
155k • written 2 days ago by
shafi98
• 0
0
votes
0
replies
61
views
CHEMBL single proteins and complexes indexing
CHEMBL
CDK1
2 days ago by
jain72744
▴ 10
0
votes
2
replies
338
views
Braker Gene Annotations Post-processing
annotations
Braker3
fungi
2 days ago by
SomeOne
▴ 270
6
votes
16
replies
8.2k
views
6 follow
STAR genome index problem
RNA-Seq
sequencing
genome
updated 2 days ago by
Ram
45k • written 7.5 years ago by
Ricky
▴ 50
2
votes
3
replies
1.4k
views
Using RepeatModeller and RepeatMasker for Multiple Gastropod Genomes: Is a Single Repeat Library Sufficient?
genome-annotation
RepeatModeller
RepeatMasker
updated 3 days ago by
SomeOne
▴ 270 • written 14 months ago by
Rohan
▴ 40
0
votes
0
replies
85
views
News:
Check our In-Person or Online NGS Data Analysis Courses for 2026
rnaseq
dnaseq
single-cell
epigenomics
nextflow
updated 3 days ago by
Ram
45k • written 3 days ago by
ecSeq Bioinformatics
▴ 20
1
vote
1
reply
266
views
Looking for bulk RNA-seq deconvolution papers
RNA-seq
Bulk
RNAseq
deconvolution
python
updated 3 days ago by
jared.andrews07
★ 19k • written 3 days ago by
AlexStar
▴ 200
0
votes
1
reply
246
views
microRNA on the NCBI
NCBI
microRNA
updated 3 days ago by
Ram
45k • written 3 days ago by
m.esmaeilpour
▴ 10
0
votes
0
replies
85
views
Gene Significance and kME cutoffs for hub genes
hub-gene
wgcna
3 days ago by
Max Zheng
• 0
0
votes
0
replies
86
views
News:
Conservation Genomics workshop - 7-10 April (online)
PopulationGenomics
SNPs
ConservationGenomics
inbreeding
4 days ago by
Physalia-courses
★ 2.7k
8
votes
4
replies
917
views
Forum:
Forum:What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2025?
bioinformatics
genomics
survey
snps
papers
10 hours ago by
Raony Guimarães
★ 1.5k
17
votes
15
replies
2.2k
views
8 follow
Tool:
Programming language trends in bioinformatics (2008–2025)
bioinformatics
programming-languages
18 hours ago by
skyresearch
▴ 30
0
votes
0
replies
91
views
Seeking feedback from users of PGAP2
panaroo
Pan-genome
roary
prokaryotic
5 days ago by
Jaykumar
▴ 50
0
votes
0
replies
116
views
Tool:
FlashDeconv: Ultra-fast spatial transcriptomics deconvolution for Visium HD (1M spots in 3 minutes)
spatial-transcriptomics
6 days ago by
Caffery
• 0
2
votes
1
reply
2.3k
views
EggNOG-mapper problem
eggnog
updated 6 days ago by
Ram
45k • written 7 months ago by
Salma
▴ 20
0
votes
0
replies
100
views
How to associate severity to sQTL
sQTL
QTLtools
6 days ago by
Priyanka
▴ 10
0
votes
2
replies
427
views
Strategy for noisy ATAC-seq: Fragment size selection for pioneer factor DA analysis
deeptools
deseq2
ATAC-seq
bam
6 days ago by
Abeer H
• 0
1
vote
3
replies
814
views
Tool:
For anyone struggling with messy single-cell data, CyteType is worth a look
Annotation
scRNA-seq
updated 7 weeks ago by
Kevin Blighe
★ 90k • written 7 weeks ago by
sukhitha.basnayake
• 0
0
votes
0
replies
169
views
Job:
Data Science Engineer at Berkeley Lab
computerscience
bioinformatics
dataengineer
machinelearning
datascience
8 days ago by
BerkeleyLab
▴ 70
1
vote
3
replies
780
views
Seeking literature on mapping 27k/450k/EPIC methylation array probes to hg38 for epigenetic aging research
methylation
hg38
epigenetics
bioinformatics
aging
updated 8 days ago by
jared.andrews07
★ 19k • written 9 days ago by
huangyiming
• 0
0
votes
0
replies
128
views
Job:
Full Time Genetics Post-doctoral Associate, University of Minnesota
Associate
Post-doctoral
8 days ago by
Al
• 0
0
votes
1
reply
286
views
News:
Virtual RAD-seq Analysis Workshop (UConn CBC, Dec. 16 -18)
Workshop
RAD-seq
Training
Variants
9 days ago by
bioadam
▴ 10
1
vote
1
reply
213
views
How can I obtain PAM50, IHC Receptor, and Expression TPM data from TCGA BRCA for RNA Seq Data
RNA-Seq
Breast
Cancer
TCGA
updated 9 days ago by
i.sudbery
22k • written 10 days ago by
Parth
• 0
0
votes
2
replies
1.2k
views
Issues with T2T in pigeon prepare from isoseq
long-read
isoseq
rna-seq
updated 9 days ago by
Zikun-Yang
• 0 • written 15 months ago by
SethJ
• 0
0
votes
0
replies
105
views
News:
Workshop: Virtual RAD-seq, January 13–16
UConn
RADseq
bioinformatics
genomics
workshop
9 days ago by
zsc25001
▴ 10
0
votes
0
replies
458
views
Runtime expectations and alternatives for vsearch --usearch_global on large nucleotide FASTA datasets
ngs
performance
vsearch
sequence-alignment
immune-repertoire
9 days ago by
emmzee
• 0
0
votes
1
reply
335
views
How to detect a duplication from IGV
duplication
coverage
mapping
IGV
updated 1 day ago by
samuel.a.odonnell
▴ 660 • written 9 days ago by
pailloufat
• 0
3
votes
1
reply
940
views
I'm trying to understand common bottlenecks in going from gene lists (RNA-seq DEGs, GWAS hits) to biological insights.
workflow
tool
pathway-analysis
literature
enrichment
updated 10 days ago by
i.sudbery
22k • written 13 days ago by
oluwafemi
▴ 10
3
votes
7
replies
912
views
Finding Transcription factors from a set of genes list
RNA-Seq
Transcription
Factor
DEGs
updated 4 days ago by
i.sudbery
22k • written 10 days ago by
rajdeepboral00
▴ 70
0
votes
0
replies
119
views
Tool:
EDTA-Audit-Tool: A smart QC utility for checking bulk EDTA (TE annotation) results
transposable_element
EDTA
quality_control
10 days ago by
Aa
• 0
1
vote
1
reply
227
views
umitools dedup and quality filtering
umitools
filtering
wgs
quality
deduplication
updated 10 days ago by
i.sudbery
22k • written 13 days ago by
song
• 0
1
vote
1
reply
211
views
RNA-seq normalization for time-dependent analysis
RNA-seq
normalization
updated 10 days ago by
i.sudbery
22k • written 13 days ago by
luca.sclisizzo
• 0
0
votes
0
replies
111
views
Calculating PRS in UKBiobank using PGSC_Calc
polygenic
pgsc_calc
genomic
ukbiobank
prs
updated 10 days ago by
GenoMax
155k • written 10 days ago by
christiantd
• 0
1
vote
0
replies
143
views
Tool:
New resource: curated plant (bell pepper, Capsicum annuum) RNASeq web portal
RNASeq
10 days ago by
Bourumir
▴ 20
15
votes
6
replies
7.7k
views
Open Reading Frame And Codons
orf
sequence
python
codon
updated 11 days ago by
CodonTable
• 0 • written 13.9 years ago by
Wilmer Garzon
▴ 60
3
votes
1
reply
327
views
Which method I should use to process cellranger data
seurat
cellplex
hashing
cellranger
updated 11 days ago by
Ram
45k • written 13 days ago by
zizigolu
★ 4.4k
0
votes
4
replies
416
views
GATK SelectVariants behavior with gvcfs
GATK
SelectVariants
gvcfs
updated 11 days ago by
Jeremy Leipzig
23k • written 13 days ago by
Gianfilippo
• 0
2
votes
4
replies
554
views
AGAT does not propagate DIAMOND functional annotations to BRAKER GFF3
diamond
annotation
braker
genomics
agat
updated 12 days ago by
GenoMax
155k • written 13 days ago by
Kinoppy
• 0
0
votes
0
replies
110
views
News:
Developing Shiny Apps with AI - online course in February
R
Shiny
Genomics
AI
13 days ago by
Physalia-courses
★ 2.7k
8
votes
8
replies
795
views
ENCODE pipelines vs Nextflow/Snakemake: design choices and use cases
pipelines
ENCODE
nextflow
snakemake
11 days ago by
DdogBoss
▴ 60
122,335 results • Page
1 of 2447
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Comment: Forum:What Are The Most Influential Bioinformatics/Computational Biology Papers
Answer: Forum:What Are The Most Influential Bioinformatics/Computational Biology Papers
Answer: Forum:What Are The Most Influential Bioinformatics/Computational Biology Papers
Answer: Exclude from analyzing rna-seq samples
Answer: Exclude from analyzing rna-seq samples
Comment: Sequencing run and batch variation
Answer: Unable to use rtracklayer import of bigwig files in older chipseq pipeline - wor
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Comment: Bioinformatics python
by
ogunjinmirashidat
• 0
Thank you very much, I am new to python. Just saw I need to create full path or put my file in python script. Thank you
Answer: Bioinformatics python
by
Mensur Dlakic
★ 30k
Three reasons come to mind: 1) the file doesn't exist; 2) the file does exist but it doesn't belong to you, so you don't have the privilege…
Comment: Forum:What Are The Most Influential Bioinformatics/Computational Biology Papers
by
Raony Guimarães
★ 1.5k
Will try to be more consistent next year. :)
Comment: Programming language trends in bioinformatics (2008–2025)
by
skyresearch
▴ 30
In addition to the repo, I recently designed a little web app to explore how programming languages in Bioinformatics have changed over time…
Answer: Exclude from analyzing rna-seq samples
by
Gordon Smyth
★ 8.6k
Have you considering doing a standard limma analysis and simply allowing limma to downweight any outlier samples? For example, `voomLmFit()…
Comment: Unable to use rtracklayer import of bigwig files in older chipseq pipeline - wor
by
awsk
• 0
Thank you for spending the time to read and reply. I tried replacing all instances of import.bw with rtracklayer::import.bw. Still the same…
Comment: Exclude from analyzing rna-seq samples
by
GenoMax
155k
> even though they are test samples, they are classified similar to control So your test samples look like controls. Based on what kind of…
Comment: Exclude from analyzing rna-seq samples
by
ATpoint
90k
I don't understand, please explain better. What I get is that you have samples, but what do you mean by QC? Like, enough reads, and things …
Comment: RNAseq results from HEK293T cells can or cannot be used for Central Nervous Syst
by
R.L.
• 0
You are so professional!
Comment: RNAseq results from HEK293T cells can or cannot be used for Central Nervous Syst
by
R.L.
• 0
Understood! Thank you so much for your help! I ve been thinking it for quite a long time!
Answer: Running psiblast on AWS with ElasticBlast
by
GenoMax
155k
If you need a per sequence PSSM file then you will need to run these as individual jobs specifying a new output file for `-out_ascii_pssm f…
Comment: Sequencing run and batch variation
by
GenoMax
155k
> but you could also check whether the sequencing machine side effect is substantial or negligible using PCA. If there was such a effect t…
Comment: Sequencing run and batch variation
by
GenoMax
155k
> The sample will come from the same prep but run again in another run. Would that also be ok to concatenate? Yes. Unless the library is …
Answer: Unable to use rtracklayer import of bigwig files in older chipseq pipeline - wor
by
ATpoint
90k
The prefixing the rtracklayer functions with `rtacklayer::` such as `rtacklayer::import.bw`. It's probably just a namespace conflict.
Answer: Sequencing run and batch variation
by
jkim
▴ 240
I think it would probably be fine to concatenate them, but you could also check whether the sequencing machine side effect is substantial o…
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