Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
120,112 results • Page
1 of 2403
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
20
views
Forum:
how to calculate Median, CV for each tissue in phased methylation patterns NGS data
CPG
2 hours ago by
Shashi Kanth
▴ 10
0
votes
2
replies
96
views
b37 liftover
b37
liftover
updated 2 hours ago by
Giulio Genovese
▴ 580 • written 10 hours ago by
spesks
• 0
0
votes
0
replies
34
views
Plugging output files from phyluce phasing workflow into Structure
phyluce
uce
bam
phasing
structure
4 hours ago by
gabe.somarriba
• 0
0
votes
0
replies
39
views
gcpp ERROR: [pbbam] read group ERROR: basecaller version is too short:
header
pacbio
bam
basecaller
gcpp
4 hours ago by
therosng
• 0
0
votes
1
reply
48
views
circos ignoring the ticks and plots
diagram
circos
updated 4 hours ago by
GenoMax
148k • written 5 hours ago by
baibhu1234
• 0
825
votes
169
replies
163k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
3.3k • written 8.1 years ago by
Istvan Albert
102k
0
votes
1
reply
108
views
Strange offsetting in deeptools?
deeptools
updated 6 hours ago by
rfran010
★ 1.3k • written 17 hours ago by
Elijah
• 0
0
votes
3
replies
93
views
Merging gvcf files between Dragen and other calling tools
gvcf
merge
bcftools
updated 6 hours ago by
Pierre Lindenbaum
165k • written 7 hours ago by
tacrolimus
▴ 140
7
votes
6
replies
243
views
Download SRA raw data using efetch
sra-toolkit
efetch
biopython
7 hours ago by
biofysikos
• 0
0
votes
7
replies
134
views
Issue with CIBERSORTx Error 139
CIBERSORTX
docker
error193
updated just now by
jared.andrews07
★ 18k • written 8 hours ago by
Hamdache
• 0
0
votes
0
replies
45
views
Repeat Modeler Database Generation
masker
modeler
genome
fungus
repeat
9 hours ago by
SomeOne
▴ 160
0
votes
0
replies
43
views
How to scale data matrix in Seurat
Scale
9 hours ago by
frarodmar17
• 0
0
votes
1
reply
78
views
Use Hi-C Sequence Data of close relative for scaffolding of genome.
assembly
genoem
fungus
HiC
sequencing
updated 7 hours ago by
GenoMax
148k • written 9 hours ago by
SomeOne
▴ 160
0
votes
1
reply
68
views
Box plot of gene expression data
boxplot
updated 8 hours ago by
ATpoint
86k • written 9 hours ago by
a.stef.44
▴ 10
1
vote
2
replies
236
views
Questions regarding GSEA - clusterProfiler
RNA-seq
GSEA
12 hours ago by
CaroH
▴ 10
0
votes
0
replies
84
views
Account for Clinical Variables in RNA-Seq Analysis
edgeR
Batch
effect
15 hours ago by
fabian
▴ 10
0
votes
2
replies
140
views
bioinformatics tutorial on Oxford
oxford
nanopore
updated 10 hours ago by
GenoMax
148k • written 19 hours ago by
Bogdan
★ 1.4k
2
votes
0
replies
87
views
Tutorial:
Step by step tutorial to replicate a genomics figure
R
Unix
ChIP-seq
bioconductor
20 hours ago by
Ming Tommy Tang
★ 4.5k
0
votes
0
replies
69
views
How to determine which pangenome nodes correspond to hg38 coordinates?
pangenome
reference-genome
hg38
genomics
23 hours ago by
a5864557
• 0
0
votes
0
replies
74
views
LDhat analysis pipeline
recombination
LDhat
1 day ago by
chaudharyc61
▴ 100
2
votes
7
replies
529
views
6 follow
Parsing error in sam file when converting to bam
samtools
bwa
fastq
bam
sam
updated 1 day ago by
GenoMax
148k • written 7 days ago by
emily.coger
• 0
4
votes
1
reply
699
views
GATK site filtering: when should I use VQSR or hard filtering?
VQSR
GATK
updated 1 day ago by
alba
• 0 • written 3.2 years ago by
samuelandjw
▴ 270
0
votes
1
reply
104
views
Missing `pro_ref` Folder in PICRUSt2 Default Files
github
PICRUSt2
updated 1 day ago by
Ram
44k • written 1 day ago by
ameeraelshinawy
• 0
2
votes
1
reply
121
views
How to Display Metadata on IGV Visualizations
Integrative-Genomics-Viewer
IGV
updated 1 day ago by
Ram
44k • written 1 day ago by
luminea
▴ 10
0
votes
3
replies
183
views
Understanding how to deal with Brain snRNA-seq data
scanpy
python
single-cell
anndata
RNA
updated 20 hours ago by
Ming Tommy Tang
★ 4.5k • written 1 day ago by
JACKY
▴ 170
2
votes
2
replies
198
views
RNA-seq combined treatment interaction experiment design
RNA-seq
DESeq2
updated 1 day ago by
Ram
44k • written 1 day ago by
Manko47
▴ 10
0
votes
0
replies
99
views
Forum:
Variant calling (SNV/InDel): is only using properly paired reads recommended?
mapping
variants
updated 1 day ago by
GenoMax
148k • written 1 day ago by
Ian
6.1k
23
votes
11
replies
16k
views
6 follow
CIBERSORT deconvolution advice
CIBERSORT
CIBERSORTx
deconvolution
updated 1 day ago by
Nguyen
• 0 • written 4.8 years ago by
joker33
▴ 150
0
votes
1
reply
261
views
News:
In-Person Workshop: Bulk RNA-Seq Data Analysis Workshop (March 24 - 27, 2025 in Halle, Germany)
Transcriptomics
Workshop
RNA-Seq
1 day ago by
ecSeq Bioinformatics
• 0
0
votes
0
replies
95
views
Sesame Data ExperimentHub and related issues
caching
sesame
methylation
updated 1 day ago by
GenoMax
148k • written 1 day ago by
jain72744
▴ 10
0
votes
0
replies
97
views
Unable to link peaks to genes for multiomics data
multiome
multiomics
linkPeaks
Signac
10X
1 day ago by
sribas.chowdhury888
• 0
0
votes
0
replies
105
views
GWAS for Klebsiella isolates
technical
help
GWAS
1 day ago by
Bahnie
• 0
0
votes
0
replies
99
views
CoCoRV - Which file from gnomAD as control
Variants
Rare
WES
2 days ago by
andrebolerbarros
• 0
2
votes
1
reply
163
views
SNP/kb in chromosome wise
Variant
SNP
Calling
updated 2 days ago by
Pierre Lindenbaum
165k • written 2 days ago by
adarsh_munna
▴ 50
0
votes
0
replies
105
views
time to event GWAS
signals
independent
updated 2 days ago by
GenoMax
148k • written 2 days ago by
JJ
• 0
3
votes
9
replies
400
views
single-cell zeros handling, inputation and filtration
zeros
single-cell
updated 1 day ago by
jared.andrews07
★ 18k • written 2 days ago by
frarodmar17
• 0
0
votes
3
replies
185
views
submitting to SRA database
files
pod5
SRA
updated 2 days ago by
ATpoint
86k • written 2 days ago by
baibhu1234
• 0
4
votes
3
replies
267
views
Flattened TSS enrichment x unique fragments from scATAC experiment
ATAC
updated 2 days ago by
jared.andrews07
★ 18k • written 3 days ago by
forestyang
• 0
1
vote
1
reply
158
views
biopython UI?
biopython
updated 2 days ago by
Joe
22k • written 2 days ago by
tada
• 0
2
votes
6
replies
294
views
determine softmask regions from FASTA
BED
FASTA
softmask
updated 1 day ago by
lieven.sterck
15k • written 2 days ago by
Matteo Ungaro
▴ 110
0
votes
4
replies
260
views
Number of reads supporting a structural variant value in Dragen structural variant calling output
Structural
VCF
variants
Manta
updated 1 day ago by
benformatics
4.1k • written 2 days ago by
ieie
▴ 10
3
votes
2
replies
315
views
Strategy for mapping rat and human gene symbols from scRNA-seq data - dealing with inconsistent nomenclature
Orthologs
scRNAseq
updated 2 days ago by
ATpoint
86k • written 3 days ago by
dxj294
• 0
0
votes
0
replies
121
views
News:
online course: R/Bioconductor for Mass Spectrometry and Proteomics
Bioconductor
R
Spectrometry
Mass
Proteomics
2 days ago by
Physalia-courses
★ 2.6k
4
votes
5
replies
290
views
What is the interpretation of sequence enrichment in whole genome sequencing?
sequencing
WGS
enrichment
updated 2 days ago by
GenoMax
148k • written 2 days ago by
marongiu.luigi
▴ 730
0
votes
3
replies
524
views
Metabat2 (binning package) Error: ReferenceFile: <filename>.fasta is not the same as in the bam headers! (targets: 10575 from the bam vs 67331 from t…
binning
metagenomics
metabat2
updated 1 day ago by
Mensur Dlakic
★ 28k • written 2 days ago by
samdegregori
• 0
0
votes
0
replies
122
views
Combining expression and mutation data from TCGA
TCGA
updated 2 days ago by
Bastien Hervé
6.1k • written 2 days ago by
Maliha
• 0
0
votes
1
reply
774
views
Annotate .fcs files with gated population classification
FACS
Flow Cytometry
FlowJo
updated 2 days ago by
Dylan
• 0 • written 4.3 years ago by
Benni
▴ 30
0
votes
0
replies
143
views
Converting map & ped files to binary file. Missing info
Map
Ped
plink
updated 2 days ago by
Ram
44k • written 3 days ago by
mulderharko
• 0
0
votes
2
replies
1.4k
views
Error in .Call2("C_solve_user_SEW", refwidths, start, end, width, translate.negative.coord
maftools
updated 3 days ago by
garcesj
▴ 50 • written 20 months ago by
alwayshope
▴ 40
1
vote
3
replies
257
views
Is there a way or a tool to compare two hmm DNA profiles?
biotool
hmmprofile
hmm-hmm
2 days ago by
abarcajose97
• 0
120,112 results • Page
1 of 2403
Recent Votes
Answer: Download SRA raw data using efetch
Comment: Download SRA raw data using efetch
Answer: Render Rmarkdown in nextflow
Answer: Questions regarding GSEA - clusterProfiler
Comment: Download SRA raw data using efetch
Answer: Download SRA raw data using efetch
Comment: Download SRA raw data using efetch
Recent Locations •
All
Mexico,
5 minutes ago
UCLA,
9 minutes ago
United States,
22 minutes ago
Australia,
25 minutes ago
Cambridge, MA,
33 minutes ago
Brazil,
34 minutes ago
Boston,
35 minutes ago
Recent Awards •
All
Popular Question
to
san96
▴ 170
Popular Question
to
tacrolimus
▴ 140
Scholar
to
GenoMax
148k
Popular Question
to
pinheirofabiano
▴ 100
Popular Question
to
Bine
▴ 90
Popular Question
to
SushiRoll
▴ 140
Popular Question
to
Bogdan
★ 1.4k
Recent Replies
Answer: b37 liftover
by
Giulio Genovese
▴ 580
Using [BCFtools/liftover](https://doi.org/10.1093/bioinformatics/btae038) will automatically take care of: - flexible contig names (e.g. …
Comment: circos ignoring the ticks and plots
by
GenoMax
148k
Please copy and paste the actual code instead of posting screenshots. You can format the text as `code` by using `101010` button in edit wi…
Answer: Strange offsetting in deeptools?
by
rfran010
★ 1.3k
It does seem like you want to set offset as 1 to return the first base of your read. Have you done something to try and remove read2? T…
Comment: Merging gvcf files between Dragen and other calling tools
by
Pierre Lindenbaum
165k
those are GVCF files, not standard VCF files, you cannot merge those files without using the INFO column.
Comment: Merging gvcf files between Dragen and other calling tools
by
tacrolimus
▴ 140
Did you not merge them all then or just rid of the INFO entirely? Many thanks!
Comment: Merging gvcf files between Dragen and other calling tools
by
Pierre Lindenbaum
165k
Hi tried to use GATK CombineGVCFs a while ago, without success, the INFO are not compatible.
Comment: Issue with CIBERSORTx Error 139
by
Hamdache
• 0
Thanks for your help I will keep you updated
Comment: Download SRA raw data using efetch
by
biofysikos
• 0
Thank you @genomax! It all makes sense (for now).
Comment: Issue with CIBERSORTx Error 139
by
GenoMax
148k
If you are able to resolve the name of the resource by doing `host cibersortx.stanford.edu` then it is possible that the method/API you are…
Comment: Download SRA raw data using efetch
by
GenoMax
148k
> I can just use curl to download the URL extracted by efetch As long as you are aware of the limitations (e.g. there may be a single file…
Comment: Issue with CIBERSORTx Error 139
by
Hamdache
• 0
Apparently yes I tried ping -c 4 google.com ping -c 4 google.com PING google.com (142.251.37.174) 56(84) bytes of data. 64 by…
Comment: Use Hi-C Sequence Data of close relative for scaffolding of genome.
by
GenoMax
148k
While someone will be along with an answer that is specific based on their experience you may want to try asking ChatGPT these two question…
Comment: Download SRA raw data using efetch
by
biofysikos
• 0
Thank you @genomax . So to recapitulate, I can just use `curl` to download the URL extracted by `efetch`. When you say ENA, do you mean th…
Comment: Issue with CIBERSORTx Error 139
by
GenoMax
148k
> Failed to get address info of cibersortx.stanford.edu: Resource temporarily unavailable Does your docker container have access to intern…
Comment: Issue with CIBERSORTx Error 139
by
Hamdache
• 0
Thank you for your response. The issue occurred while executing the following function in R: computeCBSX = function(TPM_matrix, signa…
Traffic: 3040 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6