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119,794 results • Page
1 of 2396
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Rank
Views
Votes
Replies
1
vote
1
reply
30
views
Getting fasta sequence for a gene
fasta
regulatory
genome
region
gene
updated 53 minutes ago by
ATpoint
85k • written 1 hour ago by
zizigolu
★ 4.3k
0
votes
2
replies
248
views
Is it possible to get the percentage identity between a pair of orthologs at the proteome level with the Orthology Matrix (OMA)?
with
OMA
Sequence
identity
updated 1 hour ago by
Adrian Altenhoff
★ 1.1k • written 2 days ago by
fcampbel
• 0
0
votes
0
replies
19
views
Conceptual and statistical help in creating a synthetic RNAseq cohort from a real-world cohort of samples
statistics
DESeq2
RNAseq
1 hour ago by
K.patel5
▴ 150
0
votes
2
replies
160
views
Can we construct single pangenome for different crops
pangenome
different
crops
updated 1 hour ago by
b.contreras.moreira
▴ 310 • written 2 days ago by
analyst
▴ 50
0
votes
0
replies
33
views
For RNAseq GSA analysis with unique rodent species
GOenrichment
RNAseq
GSA
hypergeometrictest
Apodemus
2 hours ago by
ohtang7
▴ 40
4
votes
2
replies
92
views
heterozygous variant on the X chromosome
xchrom
variant
vcf
heterozygous
updated 3 hours ago by
benformatics
4.1k • written 6 hours ago by
ashaneev07
▴ 50
3
votes
3
replies
124
views
Forum:
How people usually perform scRNA Seq Analysis on HPC?
Singlecell
hpc
cluster
scRNASeq
updated 3 hours ago by
ATpoint
85k • written 8 hours ago by
Tundup
• 0
820
votes
169
replies
160k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 11 weeks ago by
Biostar
3.2k • written 8.0 years ago by
Istvan Albert
102k
0
votes
0
replies
66
views
Is there a way to write a genbank file in R?
R
Genbank
Genetics
BioConductor
11 hours ago by
Jack
• 0
0
votes
3
replies
137
views
Seurat Mito Prefix Removed from Features
Seurat
updated 8 hours ago by
LChart
4.7k • written 16 hours ago by
Koki
• 0
0
votes
1
reply
87
views
dorado and modkit for m6A identification
dorado
m6A
modkit
updated 14 hours ago by
GenoMax
148k • written 14 hours ago by
baibhu1234
• 0
2
votes
4
replies
609
views
m6A modification prediction using Nanopore DRS data (RNA004)
m6A
DRS
Nanopore
14 hours ago by
baibhu1234
• 0
5
votes
9
replies
261
views
Database like Cellxgene for well-annotated atlas
mapping
reference
updated 4 hours ago by
ATpoint
85k • written 18 hours ago by
zhai
• 0
0
votes
1
reply
95
views
Insert sequence in plasmid (plasmidid)
plasmidid
insert
WGS
updated 19 hours ago by
Pierre Lindenbaum
164k • written 19 hours ago by
aLex97
• 0
2
votes
2
replies
163
views
How to remove pseudo genes from a list
Expression
gene
differential
names
14 hours ago by
Meghan.T
• 0
0
votes
3
replies
126
views
DESeq2 normalizing against two baselines
normalization
deseq2
rnaseq
updated 1 hour ago by
Devon Ryan
104k • written 20 hours ago by
seaweed96
• 0
3
votes
0
replies
91
views
Herald:
The Biostar Herald for Monday, December 09, 2024
herald
20 hours ago by
Biostar
3.2k
0
votes
2
replies
133
views
Split Visium spatial fastq according to barcodes
spatial
visium
barcodes
fastq
3 hours ago by
ThaiosX195
• 0
0
votes
2
replies
150
views
Public databases and raw counts
Normalisation
counts
databases
17 hours ago by
Luka
• 0
0
votes
0
replies
79
views
Python methylation position visualisation
python
plotting
visualisation
help
methylation
updated 21 hours ago by
GenoMax
148k • written 21 hours ago by
gmodlovver
• 0
3
votes
3
replies
226
views
Can I trust this script I wrote for assembling plant genomes?
assembly
genome.
script
plant
genomics
updated 16 hours ago by
Michael
55k • written 1 day ago by
breri
▴ 10
0
votes
1
reply
129
views
Help using enricher function from clusterProfiler
R
clusterProfiler
ORA
enrichment
updated 23 hours ago by
yura.grabovska
▴ 690 • written 1 day ago by
FJCF
• 0
3
votes
1
reply
167
views
pvalueCutoff for enrichGO, enrichKEGG and enrichDO does not seem to function properly
clusterprofiler
12 hours ago by
t.mcgovern
• 0
0
votes
2
replies
158
views
Super enhancer calling using ROSE for mm39 genome: list index out of range error
ChIP-Seq
super-enhancers
ROSE
mm39
6 hours ago by
Gayatri
• 0
0
votes
3
replies
183
views
Deducing AIRR-seq Library Generation From SRA Data
generation
SRA
airflow
primer
airrflow
updated 21 hours ago by
GenoMax
148k • written 1 day ago by
A Soggy Waffle
• 0
0
votes
0
replies
153
views
STAR pair-end gene count discrepancy vs. RSEM
rsem
htseqcount
star
genecount
2 days ago by
cropero
• 0
0
votes
2
replies
396
views
How to remove duplicated SNPs based on MAF with Plink?
SNPs
Plink2
duplication
maf
updated 2 days ago by
hakimbazol
▴ 20 • written 5 days ago by
giulia.trauzzi
▴ 30
1
vote
1
reply
211
views
linear pangenome for crops
pangenome
linear
updated 1 day ago by
Semir
▴ 50 • written 2 days ago by
analyst
▴ 50
0
votes
0
replies
161
views
On applying spike-in-derived scaling factors to ChIP-seq data: adjust for background signal (input) or not?
spike-in
deepTools
normalization
ChIP-seq
scaling-factor
2 days ago by
kalavattam
▴ 280
0
votes
2
replies
345
views
model interaction in DeSeq2 with >1K samples
DeSeq2
interaction
large
sample
set
design
updated 2 days ago by
i.sudbery
20k • written 3 days ago by
L.Grigoreva
• 0
0
votes
1
reply
240
views
Single Copy lncRNA
lncRNA
Single
Copy
updated 2 days ago by
Semir
▴ 50 • written 2 days ago by
Kutti
• 0
1
vote
6
replies
439
views
Concatenating all unmapped or alternative contigs in a reference genome
contigs
fasta
reference
updated 2 days ago by
Semir
▴ 50 • written 3 days ago by
manikin_python9f
• 0
1
vote
8
replies
551
views
Feature Counts - potential bug with outfile.jcounts
FeatureCounts
9 hours ago by
chrisk
• 0
0
votes
1
reply
283
views
log transformation before imputation (impute.knn) in proteomic data?
proteomic
log_transformation
impute.knn
updated 3 days ago by
KABILAN
▴ 130 • written 4 days ago by
Lila M
★ 1.3k
0
votes
2
replies
272
views
Spatial correlation between two continuous variables
spatial
transcriptomics
correlation
updated 3 days ago by
dsull
★ 7.0k • written 3 days ago by
hossiny
• 0
5
votes
6
replies
509
views
IGV is not showing all alignments of SAM file
IGV
3 days ago by
gernophil
▴ 120
1
vote
6
replies
375
views
Multimapping Reads to be counted or not
lowcounts
featureCounts
RNASeq
Multimapping
updated 3 days ago by
GenoMax
148k • written 3 days ago by
rajdeepboral00
• 0
0
votes
1
reply
252
views
How to create modified basecalling dataset with nanopore data with an ambiguous motif sequence?
dorado
nanopore
remora
updated 3 days ago by
GenoMax
148k • written 3 days ago by
swim1128
• 0
1
vote
2
replies
255
views
How to visualize shared pathways between ORA (enrichment) results?
visualization
ora
pathways
enrichment
3 days ago by
Picasa
▴ 650
7
votes
2
replies
293
views
How Can Pathway Analysis Methods Account for Genes with Different Activation Roles?
gsea
functional-analysis
pathway-enrichment
updated 3 days ago by
GenoMax
148k • written 4 days ago by
RoyBatty
▴ 30
0
votes
1
reply
208
views
miRNA analysis
miRNA
vescicles
extracellular
1 day ago by
deniselavezzari
• 0
3
votes
1
reply
280
views
tRNA nomenclature / numbering conventions
tRNA
RNAseq
updated 4 days ago by
microfuge
★ 2.0k • written 4 days ago by
noodle
▴ 590
0
votes
2
replies
266
views
Where can I get gtf file for Adenovirus 5?
gtf
files
virus
4 days ago by
new
▴ 10
3
votes
3
replies
349
views
Understanding STARsolo --soloStrand values and 10X scRNA-seq library structure
10X
scRNA-seq
stranded
updated 3 days ago by
dsull
★ 7.0k • written 4 days ago by
mk
▴ 300
1
vote
2
replies
237
views
The quality of the linear reference genome used for constructing a pan-genome
cactus-minigraph
4 days ago by
chiyong4783
• 0
1
vote
2
replies
408
views
HLA alignment, approximation and frequencies
Fastq
2 days ago by
oumo
• 0
0
votes
5
replies
1.1k
views
Convert RNASeq V2 data in cBioPortal having RSEM normalized results to TPM values
TPM
RNA-Seq
cbioportal
RSEM
updated 3 days ago by
dsull
★ 7.0k • written 14 months ago by
shakyaram079
• 0
0
votes
0
replies
169
views
Mutational Signatures, General Standard Refit, Cosine similarity
Standard
Refit
selected
in
signatures
4 days ago by
shakyaram079
• 0
3
votes
1
reply
246
views
Dorado for m6A modification detection
dorado
m6A
nanopore
updated 4 days ago by
GenoMax
148k • written 4 days ago by
baibhu1234
• 0
1
vote
17
replies
1.3k
views
7 follow
The BUSCO assessment of the MAKER annotation results shows a low completeness
BUSCO
MAKER
updated 3 days ago by
Michael
55k • written 5 weeks ago by
mut
• 0
119,794 results • Page
1 of 2396
Recent Votes
Answer: How people usually perform scRNA Seq Analysis on HPC?
Comment: Getting fasta sequence for a gene
Comment: heterozygous variant on the X chromosome
Answer: heterozygous variant on the X chromosome
What is the node_id in vg giraffe output (gaf or gam)?
What is the node_id in vg giraffe output (gaf or gam)?
Can I trust this script I wrote for assembling plant genomes?
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Recent Replies
Comment: Getting fasta sequence for a gene
by
ATpoint
85k
`bedtools getfasta`. You're an experienced user who has been called out for laziness many! times before, this is yet another example of zer…
Comment: DESeq2 normalizing against two baselines
by
Devon Ryan
104k
It may be helpful to know more specifically about what you mean by treatment 2 being a negative analog of treatment 1. Are these expected t…
Comment: DESeq2 normalizing against two baselines
by
Devon Ryan
104k
I'm curious how you would propose for that to work from a technical stand-point and what the resulting biological interpretation of that wo…
Answer: Is it possible to get the percentage identity between a pair of orthologs at the
by
Adrian Altenhoff
★ 1.1k
Hi, no, this is not possible as we don't store the sequence identity of all the pairwise orthologs in the OMA browser.
Comment: Can we construct single pangenome for different crops
by
b.contreras.moreira
▴ 310
In our experience, it's hard enough to compute whole genome alignments (WGA) among assemblies from the same species to even consider wider …
Comment: Is it possible to get the percentage identity between a pair of orthologs at the
by
dthorbur
★ 2.5k
I've not used OMA, but it seems simple to download query data if you're using the online platform. What's stopping you from writing a scrip…
Answer: Can we construct single pangenome for different crops
by
dthorbur
★ 2.5k
We have only just started moving into super-pangenomes which include species within a genus, typically a cultivated variety with it's wild …
Comment: heterozygous variant on the X chromosome
by
benformatics
4.1k
also worth checking for general homology genome-wide - you can BLAT the reads in IGV (maybe its in a transposable element sequence)
Answer: heterozygous variant on the X chromosome
by
benformatics
4.1k
You should start by checking if it is in the PAR region (homologous region with the Y) - https://en.wikipedia.org/wiki/Pseudoautosomal_regi…
Comment: How people usually perform scRNA Seq Analysis on HPC?
by
ATpoint
85k
I would strongly recommend a containerized solution to make things software-wise reproducible and portable.
Answer: How people usually perform scRNA Seq Analysis on HPC?
by
gglim
▴ 210
1. Set up an R Environment & install essential packages on HPC; 2. Write scripts and do some tests in local RStudio (excluding mem-inten…
Comment: Split Visium spatial fastq according to barcodes
by
ThaiosX195
• 0
Thank you for your reply @genomax ! Yes, you are right only R1. I aim to perform analyses that extend beyond spatial information, which is …
Answer: How people usually perform scRNA Seq Analysis on HPC?
by
Bastien Hervé
6.0k
You can send a job in your HPC to set up a Rstudio instance or Jupyterlab instance inside containers environments like Docker or Singularit…
Comment: Database like Cellxgene for well-annotated atlas
by
ATpoint
85k
Then ImmGen is the way to go, they have lots of data to compile your markers from at the resolution you want. I would say you don't need a …
Comment: Super enhancer calling using ROSE for mm39 genome: list index out of range error
by
Gayatri
• 0
I did update the source code wherever required, changing it to MM39, adding mm39 refseq file similar to mm10 and others. The main problem i…
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