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121,188 results • Page
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4
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7
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753
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Facing issue with output of nextflow pipeline
output
nextflow
fastqc
issue
updated 25 minutes ago by
neng
▴ 50 • written 6 weeks ago by
harsh
▴ 20
1
vote
2
replies
49
views
Pie Charts: to use or not to use
graphs
updated 1 hour ago by
Joe
22k • written 2 hours ago by
littlebioinformatician
• 0
1
vote
1
reply
57
views
Minimum Number of Cells for Downstream Analysis after subsetting a particular cell type (scRNAseq)?
cell
single
updated 3 hours ago by
ATpoint
88k • written 3 hours ago by
Tundup
▴ 10
0
votes
2
replies
82
views
Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Acinetobacter guillouiae
nif
NCBI_genome_database
Acinetobacter_guillouiae
Nitrogenase
Nitrogen_fixation
1 hour ago by
Nafi
• 0
0
votes
1
reply
60
views
Target prediction
protien
prediction
Target
updated 2 hours ago by
dthorbur
★ 3.0k • written 5 hours ago by
Samprath
• 0
5
votes
12
replies
594
views
Heatmap of a transformed deseq object with pheatmap
deseq2
pheatmap
11 hours ago by
caroline.zanchi
• 0
0
votes
0
replies
66
views
CNVkit CNVs call with threshold issues
CNVkit
threshold_log2
Somatic_variant
19 hours ago by
AIMAR
• 0
837
votes
170
replies
176k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 18 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
2
votes
2
replies
179
views
PRS result interpretation
risk
score
PRS
interpretation
polygenic
17 hours ago by
trkfs
▴ 10
0
votes
0
replies
73
views
Several errors in DROP Workflow
DROP
aberrantSplicing
FRASER
RNAseq
1 hour ago by
n_navy
• 0
1
vote
0
replies
72
views
Blog:
Setaria Pan-Genome Variation: Unraveling the Story of Domestication
pan-genome
1 day ago by
Novogene
▴ 510
2
votes
1
reply
142
views
More rare variants than common variants
PLINK
GWAS
updated 1 day ago by
LChart
4.9k • written 1 day ago by
RT
▴ 20
0
votes
1
reply
134
views
Trimmomatic command
STAR
RNASeq
Trimmomatic
updated 1 day ago by
dthorbur
★ 3.0k • written 1 day ago by
rajdeepboral00
▴ 60
1
vote
1
reply
187
views
Question about vg giraffe, vg surject and Visualization tool for mapping result
vg
updated 1 day ago by
Jordan M Eizenga
▴ 740 • written 3 days ago by
gulin
• 0
2
votes
3
replies
499
views
Where can I find somatic whole-genome or exome FASTQ files (from tumor samples) with validated variants and corresponding VCFs publicly available?
fastq
NGS
pipeline
INDELs
SNVs
updated 22 hours ago by
GenoMax
151k • written 1 day ago by
CHOCADAPASSADAEMCHOQ
• 0
0
votes
0
replies
108
views
Job:
Postdoctoral Fellow in Machine Learning and Computational Biology, The University of Memphis
PTSD
learning
bioinformatics
deep
genomics
1 day ago by
bjdaigle
▴ 10
4
votes
4
replies
484
views
Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness?
Replicates
Omics
Pooling
updated 1 day ago by
LChart
4.9k • written 6 days ago by
sardius
• 0
2
votes
1
reply
167
views
Regressing variables for finding Differentially expressed genes
batcheffect
seurat
bias
scRNASeq
updated 1 day ago by
Bastien Hervé
6.3k • written 1 day ago by
AB
▴ 390
0
votes
0
replies
150
views
Job:
Head of Bioinformatics Facility (m/f/div) at Max Planck Institute of Epigenetics
germany
e14
1 day ago by
elsalatino
• 0
2
votes
1
reply
193
views
GSEA and Cytoscape Enrichment maps
Cytoscape
RNA-seq
GSEA
updated 1 day ago by
Bastien Hervé
6.3k • written 2 days ago by
kdca
• 0
1
vote
1
reply
224
views
Alternatives to WGCNA
WGCNA
updated 2 days ago by
LChart
4.9k • written 2 days ago by
Poorvi
▴ 10
8
votes
4
replies
362
views
RNA-seq analysis
Htseq-count
HiSat2
featurecounts
STAR
updated 1 day ago by
Gordon Smyth
★ 8.1k • written 2 days ago by
SEJAL
• 0
2
votes
2
replies
1.2k
views
Liquid Biopsy datasets
RNA-Seq
next-gen
liquid biopsy
miRNA
cDNA
updated 2 days ago by
ehaag
▴ 80 • written 4.7 years ago by
pacocp
• 0
1
vote
4
replies
1.0k
views
RNA virus (HIV, HCV, Influenza, or SARS-CoV-2) datasets with corresponding fitness values.
RNA
updated 2 days ago by
ehaag
▴ 80 • written 10 months ago by
jimmysibandah
• 0
4
votes
3
replies
1.0k
views
Metagenomics mock datasets
metagenomics
updated 2 days ago by
ehaag
▴ 80 • written 16 months ago by
enuhblaise
• 0
3
votes
0
replies
166
views
News:
NCBI Comparative Genomics Virtual Codeathon, Sept 8-10.
genomics
NCBI
codeathon
1 day ago by
MirianT_NCBI
▴ 800
1
vote
1
reply
202
views
Using structure prediction approaches to predict interaction between two proteins
protein
prediction
structure
updated 2 days ago by
Mensur Dlakic
★ 29k • written 3 days ago by
Daniel
▴ 30
0
votes
2
replies
213
views
How to visualize Combat-seq corrected counts
batch-correction
combat-seq
updated 2 days ago by
cfos4698
★ 1.1k • written 2 days ago by
ybw8gh
• 0
3
votes
6
replies
343
views
Single cell expression and accessibility integration using cellxgene data
cellxgene
1 day ago by
1769mkc
★ 1.3k
0
votes
1
reply
230
views
Umbrella pathways in KEGG
KEGG
R
updated 2 days ago by
Arup Ghosh
3.3k • written 4 days ago by
Arindam Ghosh
▴ 540
0
votes
2
replies
189
views
Peptide protein dynamics
Pepdide
updated 2 days ago by
lieven.sterck
15k • written 2 days ago by
venkatramananspd
• 0
2
votes
4
replies
294
views
variant calling chromosome-wise from WGS data
wgs
updated 2 days ago by
GenoMax
151k • written 2 days ago by
analyst
▴ 60
5
votes
5
replies
296
views
Design matrix with uneven patient representation across stages
RNA-seq
design-matrix
limma
2 days ago by
Lucas
• 0
1
vote
2
replies
237
views
Forum:
The best LLM or any tool to generate legal regex expression string for specific usage?
regex
awk
sed
commands
linux
updated 2 days ago by
GenoMax
151k • written 3 days ago by
JustinZhang
▴ 140
3
votes
6
replies
2.1k
views
6 follow
minimap2 gets killed, but it doesn't explain why
minimap2
updated 2 days ago by
Arup Ghosh
3.3k • written 14 months ago by
michael.flower.14
▴ 200
0
votes
1
reply
181
views
Reference-guided transcriptome assembly using multiple SRA experiments ?
assembly
Transcriptome
projects
SRA
updated 2 days ago by
lieven.sterck
15k • written 3 days ago by
debitboro
▴ 270
5
votes
10
replies
2.8k
views
Minimap2 error in Flye de novo assembly
Flye
Minimap2
3 days ago by
Nilo
▴ 10
0
votes
0
replies
193
views
How to find hormone related proteins from a list of gene/proteins
R
updated 2 days ago by
Ram
45k • written 3 days ago by
WUSCHEL
▴ 860
0
votes
0
replies
203
views
mtDNA variants from WGS data
mitogenome
WGS
updated 2 days ago by
Ram
45k • written 3 days ago by
wonde2000
• 0
0
votes
1
reply
202
views
Merge 1000 Genome gentotype AND genotype likelihood VCFs together
VCF
LiftoverVcf
Merge
updated 3 days ago by
Giulio Genovese
▴ 630 • written 3 days ago by
JourneyToAbyss
▴ 240
0
votes
0
replies
163
views
Writing genepop from genind
R
genepop
genind
graph4lg
stacks
3 days ago by
eaabbott0
• 0
3
votes
4
replies
2.0k
views
Remove all entries with duplicate names from fastq file?
fastq
illumina
duplicate
updated 3 days ago by
Charles-Alexandre Roy
▴ 50 • written 3.9 years ago by
wormball
▴ 10
1
vote
1
reply
203
views
Copy Number Variants with CNVKit
CVNs
Somatic_variant
Recommendations
CNVKit
updated 3 days ago by
GenoMax
151k • written 3 days ago by
AIMAR
• 0
0
votes
0
replies
168
views
Basecount calculation after alignment to multi-fasta file
multi-fasta
sequence
bwa
consensus
samtool
alignment
3 days ago by
aj
• 0
0
votes
0
replies
169
views
TEtranscripts analysis
TEtranscripts
3 days ago by
frarodmar17
• 0
0
votes
0
replies
174
views
CVNkit call commande
CVNs
CNVKit
Somatic_variant
3 days ago by
AIMAR
• 0
0
votes
6
replies
387
views
FraserDataSet() error in FRASER
R
splicing
FRASER
RNAseq
alternative
21 hours ago by
n_navy
• 0
0
votes
1
reply
238
views
Strange volcano - DEGs with p.adj=0 look weird
RNA-seq
DEGs
updated 3 days ago by
manaswwm
▴ 570 • written 4 days ago by
noodlejackson
▴ 40
2
votes
3
replies
498
views
What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
motifs
atac-seq
factor
jaspar
transcription
updated 3 days ago by
GenoMax
151k • written 14 days ago by
Ambuj
• 0
0
votes
0
replies
175
views
News:
Online course: Introduction to R and Bioconductor
R
Bioconductor
Genomics
4 days ago by
Physalia-courses
★ 2.6k
121,188 results • Page
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Comment: Pie Charts: to use or not to use
NCBI Comparative Genomics Virtual Codeathon, Sept 8-10.
Comment: Minimum Number of Cells for Downstream Analysis after subsetting a particular ce
Answer: How to adjust font size of row_split labels in ComplexHeatmap R package
Answer: RNA-seq analysis
Comment: RNA-seq analysis
Answer: RNA-seq analysis
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Answer: Facing issue with output of nextflow pipeline
by
neng
▴ 50
This is a common issue that many learners encounter when working with Nextflow output management. 1. Use publishDir("${params.outdir}/..…
Comment: Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Aci
by
Nafi
• 0
Yes, I have tested all of them. I guess NCBI does not have this particular strain.
Comment: Pie Charts: to use or not to use
by
Joe
22k
As with any visualisation method, there is a time and a place for them. They are often misused, or used when a different method would be be…
Comment: Pie Charts: to use or not to use
by
Bastien Hervé
6.3k
Your first paragraph is answering the latter and as said in the second paragraph, one cannot force people not to use it. It is like RPKM/F…
Comment: Target prediction
by
dthorbur
★ 3.0k
I'm unfamiliar with the representation of phytochemicals in either database, so can't answer for certain, but generally I would say both da…
Comment: Minimum Number of Cells for Downstream Analysis after subsetting a particular ce
by
ATpoint
88k
There is no answer to this. Some people will say 10, other 3, others 500. Generally, since single-cell is noisy and has dropouts, even for …
Answer: Discrepancy Between Reported Nitrogen-Fixing Ability and Genomic Evidence in Aci
by
Mensur Dlakic
★ 29k
The specific strain described in that paper (*Acinetobacter guillouiae* EU-B2RT.R1) doesn't seem to be available in NCBI. It could be as si…
Comment: Heatmap of a transformed deseq object with pheatmap
by
GenoMax
151k
Please use `ADD REPLY/ADD COMMENT` when responding to existing posts. `ADD ANSWER` is only for new answers to original question.
Comment: Heatmap of a transformed deseq object with pheatmap
by
caroline.zanchi
• 0
...I decided to try 'ComplexHeatmap' : ```r ha = HeatmapAnnotation(df = annot_col, which="column",show_annotation_name = FALSE,show_legend=…
Comment: PRS result interpretation
by
trkfs
▴ 10
Much thanks for your reply. If I could ask - what would be the best way or what kind of data is typically needed to obtain a PRS score that…
Answer: PRS result interpretation
by
Sam
★ 4.8k
Unfortunately, PRS is a population measurement, in that, it rarely make sense to generate an individual prediction value and compared to an…
Comment: FraserDataSet() error in FRASER
by
n_navy
• 0
It looks like that; sampleID condition batch bamFile 3618-A control batch1 RP24-190-3618-A_S639_L002_2pass_Aligne…
Comment: Where can I find somatic whole-genome or exome FASTQ files (from tumor samples)
by
GenoMax
151k
Can you also include a link to the page/source where this spreadsheet came from? A random google docs link seems a bit dodgy to click on an…
Comment: Trimmomatic command
by
dthorbur
★ 3.0k
Please provide more information. You've shown a command to trim PE data, but haven't said what you're trying to achieve. But yes, trimming …
Answer: More rare variants than common variants
by
LChart
4.9k
> Is it normal to have more rare variants (MAF<0.01) than common variants in a large dataset like this? Yes, this is the site frequency sp…
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