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191 results • Page
1 of 4
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1
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4
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26
views
Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
circos
atacseq
just now by
biology_inform
▴ 50
0
votes
1
reply
34
views
Add stats to boxplot in R
stats
R
updated 23 minutes ago by
Lélé
• 0 • written 1 hour ago by
Ghada
• 0
0
votes
0
replies
18
views
Forum:
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
45 minutes ago by
yura.grabovska
▴ 70
0
votes
0
replies
15
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
41 minutes ago by
Lélé
• 0
0
votes
3
replies
34
views
Tool:
Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
Minutes
Decimal
Degrees
python
Degree
offtopic
updated 51 minutes ago by
Joe
21k • written 1 hour ago by
kuttibiotech2009
▴ 30
0
votes
2
replies
55
views
calculating genomic coverage/ base overlap in R
bioinoformatics
genomics
updated 40 minutes ago by
GenoMax
142k • written 2 hours ago by
Sayantani
• 0
0
votes
2
replies
51
views
Annotating file using bcftools
annotation
plink
bcftools
updated 2 hours ago by
Pierre Lindenbaum
161k • written 3 hours ago by
kl
▴ 10
0
votes
1
reply
50
views
genome finishing
finishing
genome
updated 43 minutes ago by
Joe
21k • written 3 hours ago by
trezini
• 0
0
votes
5
replies
128
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
19 minutes ago by
njornet
▴ 20
0
votes
3
replies
83
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
3 hours ago by
Esraa
• 0
0
votes
1
reply
75
views
DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts in whole blood: is it normal to always get NS?
rstudio
DEG
limma
updated 2 hours ago by
ATpoint
82k • written 3 hours ago by
egascon
• 0
1
vote
1
reply
80
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 4 hours ago by
ATpoint
82k • written 6 hours ago by
Alexandra
• 0
1
vote
1
reply
170
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 5 hours ago by
dariober
14k • written 1 day ago by
Holly
▴ 10
0
votes
1
reply
94
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
updated 6 hours ago by
Pierre Lindenbaum
161k • written 9 hours ago by
Arton
• 0
0
votes
0
replies
45
views
ReactomeGSA
ReactomeGSA
6 hours ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
42
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
6 hours ago by
Transmitting Science communication
▴ 70
0
votes
1
reply
67
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 2 hours ago by
GenoMax
142k • written 8 hours ago by
chrisk
• 0
0
votes
1
reply
68
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 46 minutes ago by
Joe
21k • written 10 hours ago by
iqra
• 0
0
votes
0
replies
58
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 11 hours ago by
GenoMax
142k • written 12 hours ago by
Dude
• 0
0
votes
0
replies
54
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
12 hours ago by
brunofelicianodeomena
• 0
1
vote
2
replies
143
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 7 hours ago by
colindaven
6.4k • written 14 hours ago by
mbrav005
• 0
0
votes
1
reply
105
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
10 hours ago by
sansan_96
▴ 90
0
votes
1
reply
105
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
updated 16 hours ago by
Mensur Dlakic
★ 27k • written 17 hours ago by
MarcosCosta
• 0
2
votes
2
replies
165
views
Genome Visualization Tools
bacterial
genome
updated 18 hours ago by
GenoMax
142k • written 18 hours ago by
dlera.lozano
▴ 10
2
votes
3
replies
172
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 17 hours ago by
Ram
43k • written 18 hours ago by
Prawesh
• 0
0
votes
2
replies
187
views
Using ggplotly in R
ggplot
ggplotly
11 hours ago by
jen
▴ 10
0
votes
1
reply
133
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
updated 19 hours ago by
GenoMax
142k • written 19 hours ago by
bioinfo
▴ 150
0
votes
3
replies
216
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 20 hours ago by
noodle
▴ 580 • written 23 hours ago by
doramora
▴ 10
0
votes
1
reply
119
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 20 hours ago by
LauferVA
4.2k • written 21 hours ago by
graeme.thorn
▴ 100
0
votes
2
replies
144
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
6 hours ago by
melissa.joubert
• 0
0
votes
0
replies
87
views
Calculate allelic frequency from VEP output vcf file
VEP
variant
22 hours ago by
ramiro.barrantes
• 0
4
votes
1
reply
176
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
1 day ago by
J.
▴ 40
0
votes
0
replies
87
views
Is there a real ground truth for CNV data?
CNV
1 day ago by
jennyp0706
• 0
0
votes
3
replies
182
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 1 day ago by
GenoMax
142k • written 1 day ago by
RNAseqer
▴ 270
1
vote
1
reply
121
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 20 hours ago by
Ram
43k • written 1 day ago by
kilcdincer
▴ 10
0
votes
0
replies
78
views
Retrieving ceRNA data from the starBase or ENCORI Web API
ceRNA
ENCORI
WebAPI
microRNA
starBase
updated 1 day ago by
GenoMax
142k • written 1 day ago by
Bhavya
• 0
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 1 day ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
1
vote
7
replies
351
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
10 hours ago by
ntsopoul
▴ 60
0
votes
3
replies
183
views
How to access GWAVA software of data
GWAVA
updated 1 day ago by
GenoMax
142k • written 1 day ago by
nonaddldy
▴ 10
0
votes
1
reply
158
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Chen
• 0
1
vote
1
reply
159
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Pegasus
▴ 100
0
votes
1
reply
121
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 17 hours ago by
Ram
43k • written 1 day ago by
Emily
▴ 20
1
vote
1
reply
168
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 1 day ago by
zx8754
11k • written 1 day ago by
ohtang7
▴ 40
0
votes
0
replies
85
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
1 day ago by
Spring
• 0
0
votes
2
replies
165
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
1 day ago by
IdaHao0921
• 0
0
votes
3
replies
326
views
Snakemake wrapper issue
fastqc
snakemake
updated 1 day ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
5
replies
245
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 1 day ago by
Philipp Bayer
8.5k • written 1 day ago by
林明德
• 0
0
votes
4
replies
2.3k
views
MGLTools does not work in windows 11
windows-11
Autodock
windows
MGLTools
updated 17 hours ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
4
replies
196
views
Help with IGV abbreviation
igv
updated 17 hours ago by
Ram
43k • written 1 day ago by
GeneC
• 0
0
votes
1
reply
153
views
How to process Bulk WES data?
WES
WGS
updated 1 day ago by
GenoMax
142k • written 1 day ago by
wyuan37
• 0
191 results • Page
1 of 4
Recent Votes
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
Answer: Add samples IDs to Seurat object when integrating different samples to do differ
A: RNA-Seq analysis with Python
Answer: Add samples IDs to Seurat object when integrating different samples to do differ
Add samples IDs to Seurat object when integrating different samples to do differential expression analysis
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
Answer: Getting differential ChIP-seq peaks between conditions after calling consensus p
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Recent Replies
Answer: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Papyrus
★ 2.9k
If you want to plot global accessibility, maybe you would like to plot the ATAC "signal", instead of specific peaks. In a very general mann…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Pierre Lindenbaum
161k
> I haven't been able to figure out how to generate this plot. show us what you tried and the error messages
Comment: Duplicated reads (IDs) from nanopore sequencing
by
njornet
▴ 20
I think this is the answer but I can't find in the tags info about primary and secondary alignments. I've only found in the flag that the s…
Answer: Add stats to boxplot in R
by
Lélé
• 0
Hi, Have you tried switching the order of the stat_compare_means for the Wilcox with the one for kruskall-Wallis ?
Comment: genome finishing
by
Joe
21k
I may be wrong here so someone feel free to correct me, but I've never noticed a variants file from `SPAdes`, and certainly never used one …
Comment: perseus software (version 1.5.5)
by
Joe
21k
You will need to obtain the software from an official source. I believe Perseus is a paid-for program and as such sharing via the forum wou…
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
by
Joe
21k
This post does not fit the theme of this forum.
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
by
Istvan Albert
100k
this is not bioinformatics and is not a tool and as such it is off-topic on this site
Comment: calculating genomic coverage/ base overlap in R
by
Sayantani
• 0
# Install and load necessary packages if (!requireNamespace("BiocManager", quietly = TRUE)) install.packages("BiocManager") …
Comment: Converting Degree Minutes (DM) to Decimal Degrees (DD) using python script
by
GenoMax
142k
Instead of simply posting a chunk of code it would be useful to add a line or two to say where this could would be useful. Not immediately …
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
Thanks for the link. We never use "pod5_fail" folders when re-basecalling so we did not see this issue. Current version of MinKNOW now make…
Answer: calculating genomic coverage/ base overlap in R
by
marco.barr
▴ 110
with `findOverlaps` function in `GenomicRanges` package or directly with this package `GeneOverlap`. Check out the documentation of these …
Comment: Annotating file using bcftools
by
Pierre Lindenbaum
161k
> Don't forget to follow up on your threads. If an answer was helpful, you should upvote it; if the answer resolved your question, you shou…
Answer: Annotating file using bcftools
by
Pierre Lindenbaum
161k
I think your're annotating $REF/All_20180423.vcf.gz (DBSNP isn't it ? = no genotype) with your vcf as the database ro_imputed_hrcgrch37.R2_…
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