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116,551 results • Page
1 of 2332
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0
votes
0
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11
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
18 minutes ago by
WouterDeCoster
47k
0
votes
0
replies
5
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
20 minutes ago by
Susmita Mandal
▴ 110
0
votes
0
replies
20
views
WGCNA preservation analysis
WGCNA
preservation
47 minutes ago by
michael.flower.14
▴ 180
0
votes
1
reply
22
views
Forum:
Plots for DNA methylation data
plots
DNA
methylation
updated 1 hour ago by
Basti
★ 2.0k • written 1 hour ago by
sarahawan92
▴ 10
795
votes
167
replies
141k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.6k • written 7.4 years ago by
Istvan Albert
100k
0
votes
3
replies
392
views
python file for coding potential calculator
cpc2.py
updated 1 hour ago by
atharvakarkare14
▴ 10 • written 4 days ago by
Ashok
• 0
0
votes
0
replies
33
views
Forum:
Failed kmer content
content
kmer
illumina
ngs
2 hours ago by
Kasturi
• 0
0
votes
1
reply
55
views
Heatmap and rna-seq
RNA-Seq
Heatmap
and
updated 1 hour ago by
Basti
★ 2.0k • written 4 hours ago by
qudrat.nii
▴ 10
0
votes
0
replies
52
views
Forum:
Improvement on automatic annotation of single-cell RNA-seq data from the literature using LLM
annotation
scRNA
llm
5 hours ago by
yxwucq
• 0
0
votes
0
replies
39
views
Seurat merge and batch correction
Seurat
5 hours ago by
sooni
▴ 20
0
votes
0
replies
27
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
R
Copy-number-analysis
gc.wig
genome
5 hours ago by
SSSJec
• 0
1
vote
4
replies
136
views
Redirection of Duplicate PMIDs
error
pmid
how-to
updated 6 hours ago by
LauferVA
4.2k • written 8 hours ago by
dominickd
• 0
0
votes
5
replies
172
views
How to slice a gvcf file with tabix?
Tabix
bed
gvcf
updated 10 hours ago by
Pierre Lindenbaum
161k • written 13 hours ago by
Sd
• 0
0
votes
2
replies
120
views
Help with Base quality Score Recalibration (BQSR) using GATK
GATK
BQSR
13 hours ago by
sainavyav22
• 0
0
votes
1
reply
88
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 13 hours ago by
Ram
43k • written 14 hours ago by
Cameron.walker9900
• 0
0
votes
8
replies
212
views
Error in cnetplot enrichplot package
R
updated 12 hours ago by
Ram
43k • written 14 hours ago by
Farhad
• 0
1
vote
4
replies
151
views
Is it Acceptable to Have Uniform Quality Scores in a FASTQ File?
FASTQ
updated 14 hours ago by
Mensur Dlakic
★ 27k • written 14 hours ago by
Κοσμάς
• 0
0
votes
0
replies
61
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 14 hours ago by
Ram
43k • written 14 hours ago by
maxime.policarpo
▴ 200
3
votes
3
replies
127
views
Genbank vs SRA
ncbi
genbank
genomics
sra
updated 14 hours ago by
Mensur Dlakic
★ 27k • written 14 hours ago by
c_u
▴ 520
0
votes
0
replies
49
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 14 hours ago by
Ram
43k • written 14 hours ago by
sansan_96
▴ 80
0
votes
2
replies
107
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
13 hours ago by
dxj294
• 0
0
votes
0
replies
52
views
File with NCBI summary or Uniprot description
Refseq
function
NCBI
Uniprot
protein
just now by
Amélie
• 0
0
votes
0
replies
68
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 14 hours ago by
Ram
43k • written 15 hours ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 12 hours ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
1
reply
89
views
Gene set enrichment analysis differences between 2020 and 2024
Gene-ontology
updated 16 hours ago by
ATpoint
81k • written 17 hours ago by
catherine.teyssier
• 0
2
votes
3
replies
148
views
from row count to tpm
tpm
row-count
normalization
2 hours ago by
michelafrancesconi9
▴ 20
0
votes
0
replies
60
views
Blasting two protein sequences vs two nucleotide sequences
gene-hunting
blast
updated 16 hours ago by
GenoMax
141k • written 17 hours ago by
Abeer
• 0
0
votes
4
replies
147
views
Downsampling fastq file
downsample
fastq
updated 17 hours ago by
Ram
43k • written 18 hours ago by
marco.barr
▴ 60
2
votes
3
replies
287
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 17 hours ago by
dsull
★ 5.8k • written 13 days ago by
javanokendo
▴ 60
0
votes
1
reply
99
views
tbtool
tbtool
updated 17 hours ago by
Ram
43k • written 18 hours ago by
Raman
• 0
0
votes
2
replies
145
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 16 hours ago by
i.sudbery
19k • written 19 hours ago by
Patadu94
• 0
3
votes
3
replies
170
views
Getting the nucleotide sequence of proteins, having their UniProt IDs
Nucleotide
Genomic
Sequence
Uniprot
Proteins
updated 20 hours ago by
GenoMax
141k • written 23 hours ago by
Mariana
▴ 10
0
votes
2
replies
121
views
clustalo - align milions of short seq, memory issue
memory
clustalo
updated 14 hours ago by
Mensur Dlakic
★ 27k • written 20 hours ago by
emmanouil.a
▴ 120
0
votes
1
reply
90
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 20 hours ago by
ATpoint
81k • written 20 hours ago by
enanoide
• 0
0
votes
0
replies
63
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
21 hours ago by
manaswwm
▴ 490
3
votes
3
replies
692
views
KissDE and batch effect
kissDE
kissplice
21 hours ago by
david.b.rombaut
▴ 10
0
votes
0
replies
53
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
40 minutes ago by
alifafiq1
• 0
76
votes
71
replies
19k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 21 hours ago by
GenoMax
141k • written 6.2 years ago by
Kevin Blighe
87k
0
votes
0
replies
64
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
22 hours ago by
feather-W
• 0
2
votes
3
replies
111
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
updated just now by
Pierre Lindenbaum
161k • written 22 hours ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
62
views
Annotating single cell data automatically
cell
annotation
single
22 hours ago by
Gerard
• 0
0
votes
0
replies
66
views
News:
Online course: DNA methylation
Pacbio
Nanopore
DnaMethylation
Evolution
23 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
91
views
Job:
Ensembl Plants Senior Bioinformatician
ebi
embl
genomics
ensembl
23 hours ago by
Ben_Ensembl
★ 2.4k
1
vote
2
replies
143
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
6 hours ago by
HyperEvo
• 0
0
votes
1
reply
120
views
RNA-seq bacteria contamination
RNA-seq
updated 21 hours ago by
GenoMax
141k • written 23 hours ago by
sh
• 0
0
votes
2
replies
158
views
Result of running of p3_in.pl
primer3
updated 22 hours ago by
GenoMax
141k • written 1 day ago by
nasri
• 0
0
votes
1
reply
109
views
FAM FILE
file
Fam
1 day ago by
Eleonora
• 0
0
votes
0
replies
61
views
Imputation advice
imputation
1 day ago by
kl
▴ 10
2
votes
5
replies
215
views
Per base sequence content error in RNAseq analysis
RNA-seq
analysis
updated 22 hours ago by
GenoMax
141k • written 1 day ago by
ahmad.sajad4541
• 0
0
votes
0
replies
76
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
1 day ago by
Enrique
• 0
116,551 results • Page
1 of 2332
Recent Votes
Comment: Correlation for ATAC-Seq and Chip-Seq
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Comment: PDB residue serial inconsistency and PDB id&UniProt ID mismatch
Answer: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
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Recent Replies
Comment: interpretartion of a vcf file
by
samuelkalandarov2002
▴ 10
Is it typical to observe such a profile in the context of diploid organism ?
Answer: Plots for DNA methylation data
by
Basti
★ 2.0k
Yes you can use ggplot2 to create your own plots from a table of results from a differential methylation analysis. You just need to adapt a…
Comment: Heatmap and rna-seq
by
Basti
★ 2.0k
This forum is not dedicated to this type of request, there are many online tutorials for creating heatmaps accessible with simple internet …
Answer: python file for coding potential calculator
by
atharvakarkare14
▴ 10
Download the CPC2 tool supported by python 3 from here [https://github.com/gao-lab/CPC2_standalone/releases/tag/v1.0.1][1]. Then follow …
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
let me know the scope and scale of the request (e.g. I need to do this for every record in Pubmed) and can help
Comment: Redirection of Duplicate PMIDs
by
LauferVA
4.2k
how is this query itself originating?
Comment: Redirection of Duplicate PMIDs
by
dominickd
• 0
I was able to come up with a workaround using the requests library: import requests pmid = 30134295 url = 'https://pubmed.ncbi…
Comment: What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
by
HyperEvo
• 0
Thanks for you answer! Actually I have already filtered my peak according to blacklist by bedtools. You mean it's meaningless to compare on…
Answer: Redirection of Duplicate PMIDs
by
GenoMax
141k
More than likely not since the database query seems to work for the redirected PMID but not the original. $ esearch -db pubmed -query …
Comment: DYH17 Structure Prediction
by
anasjamshed
▴ 120
Blast showed PDB: 8J07_n9(human) as best template with 62.99%. I also used swissmodel to model the protein and it showed: https://swissmod…
Comment: How to slice a gvcf file with tabix?
by
Pierre Lindenbaum
161k
No, in haplotypecaller
Comment: How to slice a gvcf file with tabix?
by
Sd
• 0
Then what is the best way to do slicing for 1Mb windows? Doing `--intervals` in the GenomicsDBImport?
Comment: How to slice a gvcf file with tabix?
by
Pierre Lindenbaum
161k
> What is your suggestion to run GenomicsDBImport efficiently? call the GVCF by slices eg: chr1:1000000-2000000<br> run GenomicsDBImport …
Comment: How to slice a gvcf file with tabix?
by
Sd
• 0
I want to run gatk `GenomicsDBImport` tool to build a GenomicsDB. I want to slice it to reduce the computation time since I have 1300 gvcf …
Comment: Problem to remove subset of patients with plink
by
chrchang523
10k
The first step has to be taken outside of PLINK here. E.g. append "_1" and "_2" to the duplicated IDs in the .ped or .fam file, then menti…
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