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116,410 results • Page
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News:
Final Call - Bioinformatics Pipeline Development with Nextflow (May 27-29, 2024)
rna-seq
workshop
dna-seq
nextflow
36 minutes ago by
David Langenberger
11k
0
votes
0
replies
17
views
GWAS Phenotypes
GWAS
54 minutes ago by
solomoncharles77
▴ 90
1
vote
1
reply
36
views
Forum:
Bioinformatics_where do i start
Sequencing
Bioinfromatics
updated 1 hour ago by
Pierre Lindenbaum
161k • written 1 hour ago by
Adi
▴ 10
0
votes
0
replies
22
views
GSEA analysis in R
GSEA
R
Arabidopsis
updated 1 hour ago by
GenoMax
141k • written 1 hour ago by
Sudip
• 0
1
vote
1
reply
28
views
Bwa sampe - BGI
BGI
Bwa-sampe
updated 1 hour ago by
GenoMax
141k • written 1 hour ago by
lorena9132
• 0
1
vote
2
replies
132
views
Visualization of PROKKA Annotation Result?
PROKKA
Annotation
updated 1 hour ago by
Joe
21k • written 1 day ago by
ferdinand
▴ 10
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 12 weeks ago by
Biostar
2.6k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
207
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
updated 3 hours ago by
ATpoint
81k • written 2 days ago by
arriyaz.nstu
▴ 30
2
votes
2
replies
111
views
I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calculated solely from the raw file (count matrix) provided in the Suppleme…
unspliced
GEO
count
matrix
velocity
4 hours ago by
Spring
• 0
0
votes
0
replies
47
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
4 hours ago by
QX
• 0
4
votes
4
replies
143
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger
scRNA-seq
10x
4 hours ago by
Spring
• 0
2
votes
3
replies
117
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
1 hour ago by
Bikram Kumar
• 0
1
vote
1
reply
215
views
WGCNA network from Adjacency or TOM matrix
WGCNA
network
updated 6 hours ago by
andres.firrincieli
3.6k • written 3 days ago by
Milly
• 0
0
votes
2
replies
121
views
Error in edgeR/Deseq2 Analysis
r
edger
updated 3 hours ago by
ATpoint
81k • written 7 hours ago by
Ravita
• 0
0
votes
2
replies
131
views
Getting marker genes for cell types
clustering
marker-genes
umap
7 hours ago by
orzrzlyo
▴ 20
0
votes
1
reply
103
views
gene body coverage with RSeqQC
rna-seq
qc
updated 13 hours ago by
jkim
▴ 170 • written 13 hours ago by
wiscoyogi
▴ 40
0
votes
1
reply
113
views
Statistical Advice Needed for RNAseq Data Analysis
Genomics
DataAnalysis
StatisticalSignificance
Bioinformatics
RNAseq
updated 3 hours ago by
ATpoint
81k • written 15 hours ago by
David
• 0
0
votes
1
reply
117
views
Using adonis to include a random effect
mixed-model
adonis
updated 16 hours ago by
LChart
3.9k • written 18 hours ago by
leranwangcs
▴ 120
1
vote
3
replies
329
views
how to get the variance explained by the independent variable from multivariate distance matrix regression model with random effect?
multivariate-distance-matrix
regression
updated 17 hours ago by
LChart
3.9k • written 1 day ago by
leranwangcs
▴ 120
0
votes
1
reply
101
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
updated 3 hours ago by
ATpoint
81k • written 17 hours ago by
bioinfo
▴ 150
0
votes
1
reply
114
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 16 hours ago by
bk11
★ 2.3k • written 19 hours ago by
sinhas
• 0
1
vote
5
replies
248
views
Best way to deal with overlapping read names in merged BAM files
picard
MarkDuplicates
18 hours ago by
shpak.max
▴ 50
0
votes
1
reply
134
views
merging Seurat objects after SCT
Seurat
SCT
updated 19 hours ago by
Ram
43k • written 20 hours ago by
michelle.swarovski
• 0
0
votes
1
reply
112
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 20 hours ago by
GenoMax
141k • written 21 hours ago by
haiying.kong
▴ 360
0
votes
2
replies
171
views
RNAseq 1 control 2 different treatment
RNA-seq
3 hours ago by
matteo.levorato
• 0
1
vote
0
replies
79
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 21 hours ago by
Ram
43k • written 21 hours ago by
Oscar
▴ 10
0
votes
1
reply
112
views
CombineGVCFs vs. MergeVcfs
CombineGVCFs
MergeVcfs
GATK
WGS
GVCF
updated 22 hours ago by
Pierre Lindenbaum
161k • written 22 hours ago by
Sd
• 0
0
votes
0
replies
72
views
News:
Deadline Approaching: PETs for Public Health Challenge
privacy
public-health-challenge
updated 21 hours ago by
Ram
43k • written 22 hours ago by
polarise
▴ 380
0
votes
0
replies
83
views
How should I make kallisto indexes?
kallisto
updated 22 hours ago by
GenoMax
141k • written 22 hours ago by
bioinfo
▴ 150
1
vote
2
replies
137
views
Problem with Sniffles pipeline and SV calling help
SV
sniffles
StructuralVariant
updated 22 hours ago by
GenoMax
141k • written 23 hours ago by
njornet
▴ 20
2
votes
0
replies
111
views
Herald:
The Biostar Herald for Monday, April 15, 2024
herald
1 day ago by
Biostar
2.6k
2
votes
1
reply
170
views
Trouble understanding seemingly contradicting results of GSE analysis (contradicting enriched GO terms with similar negative NES scores)
GSEA
pathways
GO-terms
updated 1 day ago by
i.sudbery
19k • written 1 day ago by
Manko47
• 0
4
votes
6
replies
311
views
Odd results with BLAST remote
blast
remote
NCBI
updated 6 hours ago by
b.contreras.moreira
▴ 150 • written 1 day ago by
Begonia_pavonina
▴ 150
3
votes
4
replies
267
views
BRAKER3 genome annotation
annotation
BRAKER3
genome
updated 22 hours ago by
Buffo
★ 2.4k • written 1 day ago by
manaswiniparija3
▴ 20
2
votes
0
replies
131
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
1 day ago by
Alexander
▴ 220
1
vote
1
reply
124
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 1 day ago by
GenoMax
141k • written 1 day ago by
eesiribloom
▴ 80
0
votes
0
replies
90
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
1 day ago by
Balazs Horvath
▴ 10
0
votes
0
replies
94
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
1 day ago by
adarsh_pp
▴ 40
2
votes
4
replies
283
views
Which command ro run MAKER pipeline for gene annotation ?
run.
command
to
MAKERpipeline.
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Sony
▴ 10
0
votes
0
replies
114
views
FreeBayes detection capacity
reads
freebayes
long
1 day ago by
quentinperriere
• 0
0
votes
1
reply
135
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
updated 1 day ago by
zx8754
11k • written 1 day ago by
DKA
▴ 40
0
votes
2
replies
203
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
20 hours ago by
rj.rezwan
• 0
7
votes
7
replies
668
views
Forum:
Bioinformatician who was retaliated against after reporting discriminatory harassment - Please help me navigate getting out of the situation I'm in
Career
advice
updated 20 hours ago by
Dunois
★ 2.5k • written 1 day ago by
AdviceSeeker
• 0
0
votes
0
replies
130
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
1 day ago by
Hien
• 0
0
votes
1
reply
178
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
updated 1 day ago by
zx8754
11k • written 2 days ago by
Koketso
• 0
1
vote
3
replies
373
views
Extracting data from a local NCBI taxonomy database
R
NCBI
xml
E-utilities
Blast
updated 2 days ago by
josev.die
▴ 60 • written 15 days ago by
Begonia_pavonina
▴ 150
0
votes
0
replies
160
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 1 day ago by
Ram
43k • written 2 days ago by
menyawino
• 0
0
votes
0
replies
134
views
News:
Online course: Network Analysis in R
NetworkAnalyis
R
2 days ago by
carlopecoraro2
★ 2.5k
1
vote
3
replies
267
views
Ensembl gene id conversion
biomart
ensembl
updated 3 hours ago by
ATpoint
81k • written 2 days ago by
naveedhasan2000
• 0
1
vote
2
replies
264
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 18 hours ago by
Istvan Albert
100k • written 2 days ago by
Jiang
• 0
116,410 results • Page
1 of 2329
Recent Votes
Comment: Bioinformatics_where do i start
Answer: Bwa sampe - BGI
Comment: Where to find the homopolymer regions bed file for Hg002 genome?
A: Code golf: detecting homopolymers of length N in the (human) genome
Code golf: detecting homopolymers of length N in the (human) genome
Answer: WGCNA network from Adjacency or TOM matrix
A: What Are The Most Common Stupid Mistakes In Bioinformatics?
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Recent Replies
Comment: add INFO tag to vcf with bcftools
by
Javier
• 0
Hi, im traying to do something similar, could you share the code to do what you describe. Thanks
Comment: Visualization of PROKKA Annotation Result?
by
Joe
21k
Colin's answer is essentially the right one I believe, but the more immediate consideration is: *what are you actually trying to show?* Mo…
Comment: Bioinformatics_where do i start
by
Pierre Lindenbaum
161k
https://www.biostars.org/p/9554614/ ; https://www.biostars.org/p/98983 ; https://www.biostars.org/p/9583727/ :https://www.biostars.org/p/4…
Answer: Bwa sampe - BGI
by
Pierre Lindenbaum
161k
bwa sampe produces unsorted SAM , not BAM. converting SAM to BAM will reduce the size sorting the BAM will reduce the size (you can …
Comment: Where to find the homopolymer regions bed file for Hg002 genome?
by
Bikram Kumar
• 0
Hi! Should I delete the stack exchange post? I didn't know that cross posting is bad. [https://meta.stackoverflow.com/a/425789/5140632][1] …
Answer: Visualization of PROKKA Annotation Result?
by
colindaven
6.3k
You need a genome browser and you can probably use GBK or gff3 format. Here are some suggestions - I like JBrowse best, Artemis in its …
Comment: Where to find the homopolymer regions bed file for Hg002 genome?
by
Pierre Lindenbaum
161k
cross-posted https://bioinformatics.stackexchange.com/questions/22401
Comment: Tumour purity and ploidy estimation
by
bp22
▴ 60
Hi Llyod98, This issue is still unresolved and I have not been able to find a tool or solution for purity and ploidy estimation when ther…
Comment: Ensembl gene id conversion
by
ATpoint
81k
Can you add some examples. It is hard to debug textual descriptions.
Answer: Which experiments generate Position Frequency Matrix?
by
ATpoint
81k
Yes, ChIP-seq or similar methods that assay the DNA binding of a protein. But for a reliable matrix you don't need one or two but many data…
Comment: Statistical Advice Needed for RNAseq Data Analysis
by
ATpoint
81k
> ensuring it's not merely a product of random chance If your approach of getting DEGs is a proper and sound one (e.g. DESeq2 or limma) th…
Comment: Can I compare kallisto counts from samples with different amount of reads?
by
ATpoint
81k
Unequal numbers of reads are normal, that is why normalization is needed. If you want to do simple analysis such as number of detected gene…
Comment: Error in edgeR/Deseq2 Analysis
by
ATpoint
81k
Please ask at https://help.galaxyproject.org/ which is the Galaxy help forum.
Comment: RNAseq 1 control 2 different treatment
by
matteo.levorato
• 0
yes, this is what I did. However, since my treatments are very similar each other, when I check upregulated genes in one treatment, they ar…
Comment: snakemake output directory
by
进
• 0
it is right answer
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