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186 results • Page
2 of 4
Sort: Rank
Rank
Views
Votes
Replies
1
vote
4
replies
281
views
Add stats to boxplot in R
stats
R
1 day ago by
Ghada
• 0
0
votes
1
reply
143
views
Seurat v5 and how to correctly integrate across multiple experiments
Seurat
scRNA
R
updated 20 hours ago by
Papyrus
★ 2.9k • written 1 day ago by
yura.grabovska
▴ 90
0
votes
1
reply
143
views
Difference in number of reads when using duplex and simplex base calling with Dorado
base
calling
nanopore
simplex
dorado
duplex
updated 17 hours ago by
GenoMax
142k • written 1 day ago by
Lélé
▴ 10
0
votes
4
replies
242
views
calculating genomic coverage/ base overlap in R
genomics
updated 17 hours ago by
Ram
43k • written 1 day ago by
Xbox_27
• 0
1
vote
5
replies
256
views
Annotating file using bcftools
annotation
plink
bcftools
17 hours ago by
kl
▴ 10
0
votes
9
replies
342
views
Duplicated reads (IDs) from nanopore sequencing
bam
nanopore
sequencing
1 day ago by
njornet
▴ 20
0
votes
3
replies
161
views
Problem with Calling Variants from RNA-Seq data
vcf
gatk
benchmark
giab
rna-seq
1 day ago by
Esraa
• 0
3
votes
3
replies
221
views
Getting differential ChIP-seq peaks between conditions after calling consensus peaks
MAnorm
ChIP-seq
consensus
peaks
updated 23 hours ago by
ATpoint
82k • written 1 day ago by
Alexandra
• 0
1
vote
1
reply
219
views
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
limma
updated 1 day ago by
dariober
14k • written 3 days ago by
Holly
▴ 10
1
vote
4
replies
277
views
Filtering VCF files based on VAF giving incorrect results
bcftools
GATK
Bioinformatics
picard
VCF
1 day ago by
Arton
▴ 10
0
votes
0
replies
92
views
ReactomeGSA
ReactomeGSA
1 day ago by
Shaimaa Gamal
▴ 10
0
votes
0
replies
85
views
News:
New course: Manipulation of NGS Data for Genomic and Population Genetics Analyses
KeepLearning
TScourses
1 day ago by
Transmitting Science communication
▴ 70
0
votes
5
replies
277
views
bbmerge (bbmap) ~ error with insert size file output
bbtools
bbmerge
bbmap
updated 1 day ago by
GenoMax
142k • written 2 days ago by
chrisk
• 0
0
votes
2
replies
162
views
perseus software (version 1.5.5)
preseus
mass
spectrometry
data
updated 20 hours ago by
DGTool
▴ 20 • written 2 days ago by
iqra
• 0
0
votes
0
replies
98
views
Why the shape of RCS is contradictory to the p value for nonlinearity.
RCS
ggplot2
ggplot
R
updated 2 days ago by
GenoMax
142k • written 2 days ago by
Dude
• 0
0
votes
0
replies
95
views
NEURON, Brian2, NEST, or PyNN
NEST
NEURON
PyNN
Brian2
2 days ago by
brunofelicianodeomena
• 0
1
vote
2
replies
198
views
Alphafold 3 pLDDT coloring scheme in chimerax?
ChimeraX
Alphaphold
Alphaphold3
updated 2 days ago by
colindaven
6.4k • written 2 days ago by
mbrav005
• 0
0
votes
1
reply
143
views
Polish a large genome with Pilon
Pilon
Pacbio
Polish
Illumina
2 days ago by
sansan_96
▴ 90
1
vote
2
replies
208
views
Doubt about the process of annotation, detection, identification and classification of transposable elements
annotation
TransposableElements
1 day ago by
MarcosCosta
• 0
2
votes
2
replies
197
views
Genome Visualization Tools
bacterial
genome
updated 2 days ago by
GenoMax
142k • written 2 days ago by
dlera.lozano
▴ 10
2
votes
3
replies
208
views
RSeQC : infer_experiment.py Error: Could not retrieve index file
RSeQC
RNA-Seq
updated 2 days ago by
Ram
43k • written 2 days ago by
Prawesh
• 0
1
vote
3
replies
274
views
Using ggplotly in R
ggplot
ggplotly
updated 1 day ago by
jared.andrews07
★ 16k • written 2 days ago by
jen
▴ 10
1
vote
2
replies
222
views
Why does assigning genes with biomart give me different values than using a transcripts_to_genes.txt file?
biomart
RNAseq
kallisto
16 hours ago by
bioinfo
▴ 150
0
votes
3
replies
253
views
RNAseq RNA content
mRNA
Linux
rRNA
RNA-seq
RNA
updated 2 days ago by
noodle
▴ 580 • written 2 days ago by
doramora
▴ 10
0
votes
1
reply
143
views
Post-imputation QC for input into GWAS analyses
gwas
prs
updated 2 days ago by
LauferVA
4.2k • written 2 days ago by
graeme.thorn
▴ 100
0
votes
2
replies
186
views
Using Cutadapt to trim adapters from paired-end small RNA sequence data
trimming
adapters
cutadapt
sRNA-seq
smallRNA
1 day ago by
melissa.joubert
• 0
4
votes
1
reply
200
views
Extracting only 4-fold degenerate sites from gene sequences/alignments?
alignments
2 days ago by
J.
▴ 40
0
votes
0
replies
109
views
Is there a real ground truth for CNV data?
CNV
2 days ago by
jennyp0706
• 0
0
votes
3
replies
209
views
Biomart issue, why so few 3'utrs?
utr
biomart
updated 2 days ago by
GenoMax
142k • written 3 days ago by
RNAseqer
▴ 270
1
vote
1
reply
145
views
sci-RNA-seq
Seurat
sci-RNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
kilcdincer
▴ 10
4
votes
4
replies
2.9k
views
CNVkit for somatic copy number detection
cnv
cnvkit
exome
WES
updated 2 days ago by
Anitha
• 0 • written 5.1 years ago by
stephaniem
• 0
1
vote
7
replies
379
views
Overlapping Ranges within Granges object
Genomicranges
IRanges
GRanges
2 days ago by
ntsopoul
▴ 60
0
votes
3
replies
199
views
How to access GWAVA software of data
GWAVA
updated 2 days ago by
GenoMax
142k • written 2 days ago by
nonaddldy
▴ 10
0
votes
2
replies
219
views
Inquiry about deseq2 transformation
RNA-seq
deseq2
1 day ago by
Chen
• 0
1
vote
1
reply
172
views
The total expressed genes in RNA-Seq data
RNA-SEQ
updated 2 days ago by
ATpoint
82k • written 3 days ago by
Pegasus
▴ 100
0
votes
1
reply
131
views
What is the bin size for Bamcompare?
chip-seq
deeptools
bamcompare
updated 2 days ago by
Ram
43k • written 3 days ago by
Emily
▴ 20
1
vote
3
replies
266
views
Is there any way to modify this pie chart ?
pie
ggplot
R
chart
updated 13 hours ago by
GenoMax
142k • written 3 days ago by
ohtang7
▴ 40
0
votes
0
replies
93
views
In what situations is 'outer' typically used when using anndata.concat()?
concat
anndata
scanpy
3 days ago by
Spring
• 0
0
votes
2
replies
175
views
Is it necessary to do genotype quality filteration after snp calling with GATK
snp
filteration
genotype
quality
GATK
2 days ago by
IdaHao0921
• 0
0
votes
3
replies
342
views
Snakemake wrapper issue
fastqc
snakemake
updated 3 days ago by
Wei-Chen Pan
• 0 • written 9 weeks ago by
Matvii Mykhailichenko
• 0
2
votes
5
replies
266
views
What does the 'E%' represent in BUSCO results?
BUSCO
updated 3 days ago by
Philipp Bayer
8.5k • written 3 days 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 2 days ago by
Ram
43k • written 13 months ago by
mohyeddine.taleb
• 0
2
votes
4
replies
218
views
Help with IGV abbreviation
igv
updated 2 days ago by
Ram
43k • written 3 days ago by
GeneC
• 0
0
votes
1
reply
160
views
How to process Bulk WES data?
WES
WGS
updated 3 days ago by
GenoMax
142k • written 3 days ago by
wyuan37
• 0
0
votes
1
reply
160
views
Can diamond prepdb be used to make a taxonomically aware database?
blast
diamond
taxonomy
updated 3 days ago by
GenoMax
142k • written 3 days ago by
cedric.blais
• 0
0
votes
2
replies
423
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
3 days ago by
David Langenberger
11k
0
votes
1
reply
149
views
Empty .best and .sing2 Files After Running Demuxlet
Biosciences
Demuxlet
updated 3 days ago by
Ram
43k • written 3 days ago by
eking28
• 0
2
votes
5
replies
491
views
featureCounts output summary assigned value higher than uniquely mapped reads from HISAT2
RNA-seq
featureCounts
HISAT
updated 2 days ago by
Ram
43k • written 8 days ago by
Prawesh
• 0
1
vote
3
replies
431
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
3 days ago by
kalavattam
▴ 190
1
vote
2
replies
264
views
How to interpret infinite odds ratio?
statistics
2 days ago by
Lukas
• 0
186 results • Page
2 of 4
Recent Votes
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
lncRNA and ncPEPs identification
Answer: Identifying common DEGs among multiple datasets
Answer: ggrepel function: geom_text_repel()
Comment: switch off warning in blast command line
Forward And Reverse Strand Conventions
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
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Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
Thank you very much again. I have learned a lot of things.
Comment: DEG analysis with limma and contrast matrix using multiple Parkinson's cohorts i
by
egascon
• 0
It's a microarryay experiment, not RNASeq
Comment: Sam file Header problem
by
Pierre Lindenbaum
161k
https://gatk.broadinstitute.org/hc/en-us/articles/360035890671-Read-groups
Answer: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
DGTool
▴ 20
I have also recently come across another global alignment algorithm that was recently released which could seem pretty interesting to test …
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
b.contreras.moreira
▴ 190
Not sure, you might ask in the repo, please share here the response if you find it
Answer: How to generate table_annovar from VCF input?
by
LucisTheFather
• 0
Would you be more specific to your question? Do you mean how to debug this syntax error?
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
thank you
Comment: How to extract cells of different species after mapping with combined genome?
by
Tony
• 0
I think this method should be applicable to all high-throughput single-cell RNA-seq platforms. Although the method of determining cell spec…
Comment: BiomartException: Query ERROR for existing dataset in BioMart
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▴ 10
The dataset you want (taestivum_eg_gene) exists within the "plants_mart" schema, not the default schema. Your current code assumes the defa…
Comment: Add line under stat test
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Nyksubuz
▴ 10
You could use [this][1] [1]: https://ggplot2.tidyverse.org/reference/geom_segment.html
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Nyksubuz
▴ 10
It might be because the gene symbol is not found in the KEGG database. Add some extra error handling before parsing the results or do a man…
Comment: Sam file Header problem
by
saifulislam99121
• 0
Thank you for your reply. I am not very much sure about this RG. Can you explain me a bit?
Comment: GRIDSS: the Genomic Rearrangement IDentification Software Suite
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It seems that Alexandrov's [structural variant and copy number signatures][1] estimated by the [SigProfiler software ecosystem][2] aren't c…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
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142k
Then you may want to see if a program like `lastz` ([**LINK**][1]) may be useful. [1]: https://github.com/lastz/lastz
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43k
What is the purpose of this tool? I have `~/bin` in my $PATH and I soft-link all executables I need to that location so why install a new t…
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