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120,698 results • Page
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News:
Live Online Course: Introduction to Python, April, 2025
python
programming
course
1 hour ago by
soledad.esteban
• 0
3
votes
6
replies
408
views
Multiple factors in DESeq2
deseq2
3 hours ago by
noodlejackson
▴ 30
3
votes
2
replies
144
views
Why do RNAseq reads align to non-gene regions of the bacterial genome?
RNAseq
transcription
updated 4 hours ago by
i.sudbery
21k • written 1 day ago by
Texx
▴ 30
1
vote
1
reply
50
views
Confused about discovering novel genes in a model organism using STAR, Trinity, and reference genomes
star
trinity
rnaseq
updated 4 hours ago by
Ram
45k • written 4 hours ago by
zizigolu
★ 4.3k
835
votes
169
replies
170k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 months ago by
Biostar
3.4k • written 8.3 years ago by
Istvan Albert
102k
3
votes
6
replies
96
views
nanopore variant calling
pacBio
long-read
nanopore
2 hours ago by
Meghan.T
• 0
0
votes
2
replies
103
views
enrichGo problem
enrichGo
3 hours ago by
mimijane1664
• 0
1
vote
4
replies
126
views
Seeking Help for Reanalysis of Raw WES Data
WES
updated 1 hour ago by
Jeremy Leipzig
23k • written 10 hours ago by
lidia.manczak
• 0
1
vote
8
replies
156
views
Biscuit Alignment and Index failed - WGBS - Bisulfite analysis
BWA
Biscuit
Bisulfite
updated 5 hours ago by
Ram
45k • written 10 hours ago by
Palanikumar.Palanichamy
• 0
0
votes
3
replies
133
views
illumina: Adapter Confusion
ILLUMINA
ADAPTER
updated 9 hours ago by
GenoMax
149k • written 12 hours ago by
lingjun meng
▴ 20
2
votes
2
replies
115
views
Identifying primer sequences from raw FASTQ files
primers
updated 7 hours ago by
michael.ante
★ 4.0k • written 13 hours ago by
Chandini
• 0
2
votes
7
replies
1.2k
views
HTSlib threads when ingesting large bgzipped FASTA
htslib
samtools
bgzip
c
updated 8 hours ago by
aw7
▴ 370 • written 20 months ago by
Oleksii
• 0
3
votes
3
replies
191
views
question for dowloading Protein fasta sequence by edirect using while
edirect
updated 19 hours ago by
vkkodali_ncbi
★ 3.8k • written 1 day ago by
诗友
• 0
1
vote
2
replies
605
views
Validate RNAseq Models in Microarray Data?
microarray
rnaseq
coxlasso
fpkm
updated 7 hours ago by
ATpoint
87k • written 2.7 years ago by
vitor
▴ 130
0
votes
0
replies
70
views
Restrict anlaysis of WGS VCF file to Refseq Select using snpeff
refseq
vcf
wgs
23 hours ago by
Gabriel
• 0
0
votes
0
replies
77
views
How to clarify results from an HLA association analysis - Omnibus tests/HATK/other options
Omnibus
HLA
HATK
GWAS
Regression
1 day ago by
s.may-wilson
▴ 50
0
votes
2
replies
146
views
Novel genes in model organisms
homologue
genome
gene
1 day ago by
zizigolu
★ 4.3k
0
votes
1
reply
153
views
Understanding sctransform
sctransform
Seurat
updated 1 day ago by
Bastien Hervé
6.1k • written 1 day ago by
Deepak Tanwar
★ 4.2k
1
vote
1
reply
171
views
Subset reads based on Phred-score ranges
phred
sequencing
ngs
updated 1 day ago by
GenoMax
149k • written 1 day ago by
Mark
▴ 30
4
votes
1
reply
162
views
Reasoning - Why is it invalid to compare ratios of TPMs?
RNAseq
analysis
expression
normalization
differential
TPM
batch
effect
updated 1 day ago by
ATpoint
87k • written 1 day ago by
VTh
• 0
2
votes
2
replies
254
views
DEGs Analysis For a Microarray Data that has one biological replicates per cell line in each condition
Analysis
DEGs
Microarray
1 day ago by
mete.han.celebi
• 0
2
votes
6
replies
292
views
The soapdenovo2 genome assembly is highly fragmented - learning genome assembly with public data
Gene
soapdenovo2
assembly
updated 1 day ago by
lieven.sterck
15k • written 1 day ago by
JieQY
• 0
0
votes
2
replies
158
views
Cytoscape COLOUR EDGES
Reulatory
Cytoscape
Networks
9 hours ago by
SKY
▴ 60
3
votes
3
replies
464
views
VCF filtering with Allele Balance (AB) using FilterVcf (Picard)
Allele-Balance
FilterVcf
Picard
GATK
updated 1 day ago by
GokalpC
▴ 160 • written 14 days ago by
Eduardo
▴ 20
1
vote
4
replies
497
views
Haplotype analysis
founder
haplotype-analysis
6 hours ago by
disha3786
• 0
3
votes
4
replies
296
views
Indica rice genome and annotation files
RNASeq
updated 1 day ago by
ChanderKant (CK) Chaudhary
▴ 10 • written 3 days ago by
chandimaa
• 0
2
votes
6
replies
338
views
Question: Making primers for cloning and transfection
transfection
cloning
primer
PCR
gene
updated 1 day ago by
jared.andrews07
★ 18k • written 2 days ago by
Lu Adr
• 0
0
votes
0
replies
120
views
Help with the interpretation of Silhouette width averaging
clustering
kmeans
cluster
silhouettemethod
2 days ago by
Maria Jose
• 0
0
votes
1
reply
182
views
Job:
Open Rank Tenure-earning Faculty in the Department of Biostatistics & Bioinformatics
Cancer
Oncology
Tenure-earning
Faculty
Bioinformatics
updated 2 days ago by
GenoMax
149k • written 2 days ago by
maritza.garcia-saavedra
• 0
0
votes
1
reply
169
views
Job:
Open Rank Tenure-earning Faculty in the Department of Biostatistics & Bioinformatics
Oncology
Faculty
Leadership
updated 2 days ago by
GenoMax
149k • written 2 days ago by
maritza.garcia-saavedra
• 0
35
votes
14
replies
1.2k
views
12 follow
Forum:
How do you estimate time to complete a project or task?
career
ngs
written 6 weeks ago by
sviatoslav.kendall
▴ 960
0
votes
0
replies
172
views
Tutorial:
CC-By 4.0 Project (unpublished papers and data) release on OSF - Discoveries of 2nd/3rd order gene combinations for static/time series data in cell/…
MachineLearning
GeneCombination
CellSignaling
SensitivityAnalysis
21 hours ago by
sinha.shriprakash
▴ 20
1
vote
1
reply
163
views
Pre-Alignment process
read_depth_measure
updated 2 days ago by
GenoMax
149k • written 2 days ago by
AIMAR
• 0
0
votes
0
replies
132
views
Differential methylation analysis using Dorado
dorado
m6A
DRS
nanopore
2 days ago by
baibhu1234
▴ 20
0
votes
0
replies
121
views
Annotate Phylogentic Tree with classes
python
tree
phylogenetic
analysis
2 days ago by
BIANCA
• 0
1
vote
1
reply
169
views
Is it possible for genomic DNA to be sequenced in a modern RNA-seq protocol?
transcriptome
genome
RNA-seq
updated 2 days ago by
GenoMax
149k • written 2 days ago by
predeus
★ 2.1k
0
votes
1
reply
156
views
Help with CIBERSORTx Error in Single-Cell RNA-seq Analysis: Invalid 'times' Argument
cibersortx
updated 2 days ago by
jared.andrews07
★ 18k • written 2 days ago by
Pumla
• 0
2
votes
3
replies
249
views
Picard gives empty value for HS_LIBRARY_SIZE when running CollectHsMetrics
sequencing
library
picard
1 day ago by
Bertalan_Takacs
▴ 120
1
vote
2
replies
211
views
single cell compositional analysis - how adjusting for covariates (age)
compositional-analysis
RNA-seq
single-cell
11 hours ago by
Francesco
▴ 20
0
votes
1
reply
169
views
Differential Expression Analysis of scRNA seq data with Pseudobulking
edgeR
scrnaseq
pseudobulking
updated 2 days ago by
ATpoint
87k • written 2 days ago by
Sophia
• 0
9
votes
20
replies
7.4k
views
11 follow
BLAST Database error: Database memory map file error
makeblastdb
updated 1 day ago by
tony_s
▴ 10 • written 6 months ago by
Martina
• 0
0
votes
0
replies
126
views
News:
Last Two Spots Available – R/Bioconductor for Mass Spectrometry & Proteomics
Proteomics
Bioconductor
Mass-Spectrometry
R
updated 2 days ago by
Ram
45k • written 2 days ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
121
views
News:
Last-Minute Open Spots for Our RNA-Seq Workshops!
single-cell
transcriptomics
scRNAseq
RNAseq
updated 2 days ago by
Ram
45k • written 2 days ago by
ecSeq Bioinformatics
▴ 10
2
votes
2
replies
339
views
advice on rooting a tree in R
R
tree
ggtree
phylo
1 day ago by
Matteo Ungaro
▴ 110
0
votes
1
reply
217
views
Beagle removed many sites in the target dataset after imputation
genotype
beagle
imputation
2 days ago by
LCG
• 0
0
votes
0
replies
112
views
Blog:
Novogene Single-cell and Spatial Multi-omics Case Study: Application in Immunosenescence
Single-cell
2 days ago by
Novogene
▴ 500
0
votes
2
replies
807
views
ArchR error Error in grid.Call.graphics(C_downvppath, name$path, name$name, strict): Viewport 'Norm. Enrichment -log10(P-adj) [0-Max]_heatmap_body_1_…
ArchR
2 days ago by
Bioinformatics_16
• 0
3
votes
5
replies
6.1k
views
normalization to "housekeeping" genes of RNAseq data vs qPCR result
qPCR
RNAseq
updated 2 days ago by
Conor
• 0 • written 3.6 years ago by
cwwong13
▴ 40
0
votes
12
replies
700
views
MD5 Mismatch on chrY When Extracting CRAM Region Despite Correct Reference Genome
reference-genome
updated 3 days ago by
GenoMax
149k • written 5 days ago by
offset
• 0
2
votes
8
replies
2.7k
views
6 follow
Normalizing TCR data
Analysis
updated 3 days ago by
apontel
• 0 • written 6.1 years ago by
ruchitkpanchal
• 0
120,698 results • Page
1 of 2414
Recent Votes
Answer: Seeking Help for Reanalysis of Raw WES Data
Comment: Identifying primer sequences from raw FASTQ files
Answer: Multiple factors in DESeq2
Comment: CNVKit for unmatched tumor-only WGS samples
Answer: nanopore variant calling
A: How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental
Answer: nanopore variant calling
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Popular Question
to
Daniel
▴ 30
Scholar
to
GenoMax
149k
Supporter
to
Meghan.T
• 0
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pt.taklifi
▴ 60
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Dunois
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WouterDeCoster
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Alx
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Recent Replies
Comment: Seeking Help for Reanalysis of Raw WES Data
by
Jeremy Leipzig
23k
there is live help on the sarek slack in nf-core https://nf-co.re/join/slack
Comment: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair
by
marongiu.luigi
▴ 740
Is there a citation for this package? Thank you
Answer: Multiple factors in DESeq2
by
noodlejackson
▴ 30
Just an update, DESeq2 works using GLM and cannot consider random factors like patient ID when patient ID groups are unique to outcome fact…
Comment: enrichGo problem
by
mimijane1664
• 0
Hiya, yes, they do have GO terms associated with them but thanks for the suggestion! I had already actually checked them using Panther but…
Answer: Why do RNAseq reads align to non-gene regions of the bacterial genome?
by
i.sudbery
21k
As Mensur Dlakic noted, bacteria have 3 and 5' untranslated regions like any other organism. The polymerase absolutely doesn't stop at the …
Comment: nanopore variant calling
by
Meghan.T
• 0
Awesome thanks a lot!
Comment: nanopore variant calling
by
GenoMax
149k
Now `dorado` is the default basecaller for MinKNOW. https://github.com/nanoporetech/dorado It is performant on the right GPU but in a pinc…
Comment: nanopore variant calling
by
Meghan.T
• 0
Thanks! As I understand this workflow is for variant calling, right? I was wondering if you could kindly suggest some tools for ***basecall…
Comment: nanopore variant calling
by
GenoMax
149k
See the link I added above.
Comment: nanopore variant calling
by
Meghan.T
• 0
Thank you so much @GenoMax . Can you advise me on the basecalling tools for nanopore? I believe the company sends the fastq files but I mig…
Comment: Confused about discovering novel genes in a model organism using STAR, Trinity,
by
Ram
45k
I think STAR can detect novel fusion genes and splice junctions but I'm not sure about novel "genes" as such.
Answer: nanopore variant calling
by
GenoMax
149k
Using Nanopore would be a good option though you have to keep in mind that the error rate will be slightly higher than illumina. If you hav…
Comment: PIASO, a python toolkit for single-cell data analysis
by
Min
• 0
The issues were now fixed in piaso-tools v1.0.1 in PyPI and cosg v1.0.3 in PyPI. Thank you for your feedback and suggestion!
Comment: Seeking Help for Reanalysis of Raw WES Data
by
lidia.manczak
• 0
Thank You :)
Comment: enrichGo problem
by
Buffo
★ 2.4k
Have you checked if any of those genes have GO terms? You can try using the [GO ontology database][1]. [1]: https://geneontology.org/
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