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109,102 results • Page
1 of 2183
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0
votes
1
reply
16
views
Time change in expression vs time change in phenotype
RNA-Seq
DGE
DESeq2
32 minutes ago by
Ivan
• 0
0
votes
0
replies
13
views
How to perform a gsva assessing for the directonality of the genes.
gsva
51 minutes ago by
roybatty269
• 0
0
votes
4
replies
817
views
activity of unloaded/unassembled Tn5
sequencing
next-gen
updated 32 minutes ago by
ATpoint
70k • written 5.1 years ago by
zhaohainancau
• 0
4
votes
7
replies
235
views
Nextflow rnaseq finishing early
RNA-seq
nextflow
updated 3 minutes ago by
Ram
38k • written 1 hour ago by
Raygozak
★ 1.4k
3
votes
6
replies
315
views
ClusterProfiler enrichKEGG – remove organism name in plots?
KEGG
ggplot2
enrichKEGG
ClusterProfiler
updated 10 minutes ago by
jv
★ 1.0k • written 6 days ago by
Sian
▴ 20
1
vote
3
replies
154
views
differential gene analysis
DGE
updated 1 hour ago by
Ram
38k • written 9 hours ago by
kalyani
• 0
0
votes
1
reply
17
views
syntax errors when running part3 all-against-all
error
AssertDatabaseVersionsInSync
syntax
all-against-all
updated 1 hour ago by
Ram
38k • written 1 hour ago by
Sofia
• 0
1
vote
0
replies
37
views
Herald:
The Biostar Herald for Tuesday, March 28, 2023
herald
2 hours ago by
Biostar
1.6k
1
vote
4
replies
403
views
Retrieve protein sequence from Mgnify given only accession code
Mgnify
API
updated 2 hours ago by
biomarco
▴ 20 • written 9 months ago by
jscience
• 0
1
vote
1
reply
153
views
Browsing MGnify IDs and clusters
metagenomics
mgnify
ebi
2 hours ago by
biomarco
▴ 20
0
votes
0
replies
28
views
calculation of calibration factors using impuation reference panel and ethnicity
GWAS
Calibration
factor
3 hours ago by
parveenkayenat
• 0
1
vote
3
replies
94
views
Artificial reads - remove multiple mapped reads against reference genome, and only keep reads that completely match without any mismatches - samtools
samtools
updated 2 hours ago by
GenoMax
127k • written 3 hours ago by
Agamemnon
▴ 60
0
votes
0
replies
28
views
Haploview linkage format .ped and .info file error
plink
Haploview
vcftool
3 hours ago by
Nai
▴ 50
0
votes
0
replies
40
views
Clustering with monocle 3
scRNA-seq
trajectory
analysis
3 hours ago by
Eisuan
▴ 20
5
votes
1
reply
112
views
what is IGV visualization lighter color variants stand for
visualization
vcf
IGV
updated 4 hours ago by
Jorge Amigo
14k • written 8 hours ago by
zhangfish
▴ 40
0
votes
2
replies
1.5k
views
Error when changing the database for minfi dropLociWithSnps
SNP
minfi
methylationEPIC
illumina
methylation
updated 5 hours ago by
Satu
• 0 • written 5.7 years ago by
Ellen O
▴ 20
730
votes
161
replies
108k
views
100 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 13 days ago by
Biostar
1.6k • written 6.3 years ago by
Istvan Albert
97k
0
votes
0
replies
61
views
How to export GWAS lists available in Open Targets database
GWAS
phenotype
openTargets
gene
5 hours ago by
dzisis1986
▴ 60
0
votes
0
replies
59
views
Bcftools consensus generates mismatched consensus sequence
Consensus
sequence
6 hours ago by
Duy
• 0
0
votes
0
replies
44
views
Is there a function to get the number of aligned sites between pairs of sequences in a multiple sequence alignment in R?
msa
R
6 hours ago by
audrey
• 0
0
votes
0
replies
54
views
Nucleotide substitution model and neighbor-joining tree
phylogeny
substitution
mega
neighbor-joining
modeltest
6 hours ago by
poecile.pal
▴ 50
2
votes
4
replies
236
views
Most efficient way to run Diamond against a very very large database (i.e., NCBI's NR)?
protein
annotation
alignment
diamond
nr
updated 3 hours ago by
GenoMax
127k • written 17 hours ago by
O.rka
▴ 650
0
votes
0
replies
61
views
Octopus advanced vcf guide: Example of overlapping vcf calls with *
vcf
spanning
alleles
octopus
9 hours ago by
penington.j
• 0
0
votes
0
replies
81
views
how can we improve genome assembly levels ? from contig to complete using bioinformatics pipelines?
contig
genome
pipelines
assembly
updated 1 hour ago by
Ram
38k • written 9 hours ago by
vasudhapai
• 0
3
votes
3
replies
183
views
Editing fasta headers
fasta
updated 1 hour ago by
Ram
38k • written 12 hours ago by
Zoe
• 0
0
votes
0
replies
85
views
Link products to their genes
RNA-SEQ
GO
edgeR
10 hours ago by
Pegasus
▴ 80
0
votes
0
replies
88
views
Trajectory analysis using Monocle3 with Seurat sub-clustering
scRNA-seq
Trajectory
Seurat
analysis
Monocle3
14 hours ago by
joonhong kwon
▴ 40
0
votes
0
replies
94
views
News:
The Canadian Bioinformatics Workshops are back for summer 2023
CBW
training
workshop
16 hours ago by
bioinformatics.ca
• 0
0
votes
1
reply
141
views
Error parsing strand (?) from GFF line
assembly
updated 10 hours ago by
cmdcolin
★ 2.9k • written 16 hours ago by
hafiz.talhamalik
▴ 350
0
votes
0
replies
85
views
Variant caller reports a homozygous variant genotype, but more reads are associated with reference
bcftools
variants
15 hours ago by
rebeliscu
▴ 50
0
votes
3
replies
214
views
Sample size for population genetics
Population-genetics
sample-size
updated 16 hours ago by
Jeremy Leipzig
21k • written 21 hours ago by
zimmer.schweiz
• 0
1
vote
0
replies
109
views
List of Ongoing and Planned Long Read Sequencing studies?
long-read-sequencing
third-generation
updated 21 hours ago by
Ram
38k • written 21 hours ago by
Vincent Laufer
★ 2.5k
3
votes
8
replies
3.8k
views
counting the unmapped reads
RNA-Seq
updated 22 hours ago by
chemkhi.ali13
• 0 • written 7.9 years ago by
fi1d18
★ 4.1k
0
votes
1
reply
132
views
SNP ID (rsID) to Chr no. and Position
Annotation
21 hours ago by
Jewahir
• 0
0
votes
0
replies
101
views
how to plot distribution of SNPs across a set of genes based on distance between snp and gene
snp
genes
updated 21 hours ago by
Ram
38k • written 22 hours ago by
rheab1230
▴ 140
0
votes
0
replies
92
views
Reactome Species Comparison - analysis table
reactome
4 hours ago by
a11msp
▴ 120
0
votes
1
reply
182
views
Discordinant aligment
Paired-end
HISAT2
updated 23 hours ago by
Istvan Albert
97k • written 1 day ago by
ali
• 0
0
votes
1
reply
133
views
Using multimaping reads or unique reads on featurecounts?
featurecounts
HISAT2
updated 23 hours ago by
GenoMax
127k • written 1 day ago by
omargmc.tak
• 0
0
votes
0
replies
96
views
News:
Next-Generation Sequencing Data Analysis: A Practical Introduction (May 3-5, 2023 in Munich, Germany)
NGS
DNA-Seq
calling
RNA-Seq
workshop
variant
1 day ago by
David Langenberger
9.9k
0
votes
1
reply
249
views
module and trait correlation for WGCNA
treatment
WGCNA
relation
microarray
module-treatment
updated 1 day ago by
andres.firrincieli
3.1k • written 2 days ago by
Shriyansh
• 0
3
votes
7
replies
227
views
1000 genomes hg38 with dbSNP rsid
1000genomes
dbsnp
updated 22 hours ago by
Ram
38k • written 1 day ago by
Vince
▴ 150
0
votes
0
replies
85
views
How to import impute2.dosage files to analyse it in R (GWAS)
regression
GWAS
impute2
dosage
1 day ago by
Sebastian
• 0
5
votes
3
replies
408
views
What's the correct way to map to hg38 with alternative contigs?
NGS
bwa
1 day ago by
Belanov
▴ 10
6
votes
4
replies
169
views
Download NCBI compiled protein database for specific genus
protein
NCBI
updated 1 day ago by
GenoMax
127k • written 1 day ago by
saadleeshehreen
▴ 110
0
votes
0
replies
91
views
Michigan Imputation server failed job
michigan-imputation-server
vcf
updated 1 day ago by
Ram
38k • written 1 day ago by
Najla
• 0
0
votes
0
replies
93
views
MD simulation error
MD
schrodinger
updated 1 day ago by
Ram
38k • written 1 day ago by
mixmatchey
• 0
0
votes
0
replies
99
views
File has zero value indivuals
Haploview
updated 1 day ago by
Ram
38k • written 1 day ago by
Nai
▴ 50
0
votes
3
replies
253
views
Kallisto bustools for scRNA-seq
Kallisto
6 hours ago by
t.ru
• 0
0
votes
0
replies
125
views
KEGGList Error in R
KEGGList
1 day ago by
GiV17
▴ 50
0
votes
1
reply
212
views
How to analyze RepeatProteinMask results
RepeatProteinMask
1 day ago by
zijian
• 0
109,102 results • Page
1 of 2183
Recent Votes
Comment: Artificial reads - remove multiple mapped reads against reference genome, and on
The Biostar Herald for Tuesday, March 28, 2023
A: Where to find targets.txt in GEO dataset.
Comment: Nextflow rnaseq finishing early
Comment: Nextflow rnaseq finishing early
Comment: Nextflow rnaseq finishing early
Comment: Download NCBI compiled protein database for specific genus
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ashwing.kofficial
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127k
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Recent Replies
Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
by
jv
★ 1.0k
Just giving OP some options since they didn't show their code. In my case I am using `clusterProfiler::download_KEGG` to download KEGG gene…
Comment: Time change in expression vs time change in phenotype
by
Ivan
• 0
Worst case we could use DEseq2 to associate (E_t2 - E_t1) with I(t), where I(t) is an indicator variable, =1 at t1 and =2 at t2… So now we …
Comment: activity of unloaded/unassembled Tn5
by
ATpoint
70k
Appreciate your efforts but this is all off-topic here. Suggest to put this in a GitHub Pages or similar location to make it accessable for…
Comment: Nextflow rnaseq finishing early
by
ATpoint
70k
Regardless, you can ask this at nf-core slack which has a dedicated channel for this pipeline. https://nf-co.re/join/slack => channel…
Comment: Nextflow rnaseq finishing early
by
ATpoint
70k
Be nice to people...you have the problem and lack expertise to solve it, not the people trying to help you.
Answer: activity of unloaded/unassembled Tn5
by
callumjcparr
• 0
![enter image description here][1] Example of TapeStation of scaled-up reaction in 500,000 nuclei. Working on the assumption we usually …
Comment: Nextflow rnaseq finishing early
by
Raygozak
★ 1.4k
You're asking me? why do you think i'm here asking if i hadn't checked everything else?
Comment: Nextflow rnaseq finishing early
by
Raygozak
★ 1.4k
it's in the command line.
Comment: Nextflow rnaseq finishing early
by
Ram
38k
> the RNA-seq pipeline from nextflow **which** RNA-seq pipeline? Can you add a link to it please?
Comment: Nextflow rnaseq finishing early
by
Pierre Lindenbaum
153k
is there any step that depends of the QC ? eg: MULTIQC_TSV_FAIL_TRIMMED or MULTIQC . what happens if any QC fails ?
Answer: ClusterProfiler enrichKEGG – remove organism name in plots?
by
e.r.zakiev
▴ 30
before invoking `dotplot` function replace the parts of the strings in your `enrichKEGG` result (let's call it `ekegg`): `ekegg@result$D…
Comment: syntax errors when running part3 all-against-all
by
Ram
38k
What on earth are you talking about? Please add some context, we are not mind readers.
Answer: differential gene analysis
by
ATpoint
70k
It is impossible to tell anything about these plots as code is missing. As said already, standard tests such as t-tests and Wilcox tests ar…
Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
by
e.r.zakiev
▴ 30
When using `enrichKEGG` function with the default parameters (`ekegg <- enrichKEGG(gene = ENTREZID_genes, organism = 'mmu', pvalueCutoff = …
Comment: differential gene analysis
by
kalyani
• 0
i have used DESeq2 but same issue. if u have a reference for these please share.
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