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194 results • Page
4 of 4
Sort: replies
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Views
Votes
Replies
0
votes
1
reply
218
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
updated 1 day ago by
Ram
41k • written 7 days ago by
bioinfo
▴ 60
1
vote
1
reply
205
views
How should I run ssgsea analysis ?
functional
TPM
enrichment
gsea
ssgsea
updated 3 days ago by
singh.vijender
▴ 110 • written 3 days ago by
DareDevil
★ 3.3k
0
votes
1
reply
151
views
VCF conservation into Treemix
Treemix
Plink
VCF
updated 3 days ago by
singh.vijender
▴ 110 • written 3 days ago by
reza
▴ 300
0
votes
0
replies
128
views
Mapping Mouse RNAseq Marker Genes to Reactome Pathways
single-cell
pathways
reactome
RNAseq
gene
2 days ago by
el24
▴ 40
0
votes
0
replies
116
views
deeptools k-means clustering
heatmap
deeptools
chipseq
2 days ago by
biology_inform
▴ 50
0
votes
0
replies
30
views
Job:
Postdoc in comparative genomics of plant-associated bacteria (Polytechnic University of Madrid, SPAIN)
evolution
genomics
mutation
bacteria
genomes
3 hours ago by
Alejandro
• 0
0
votes
0
replies
102
views
CHIPSEQ Analysis , DiffBind Parameters
DiffBind
ChIP-seq
2 days ago by
DINESHR
• 0
0
votes
0
replies
106
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle
protein
alignment
2 days ago by
Richard Fontaine
• 0
0
votes
0
replies
99
views
sequencing deep mutational scanning library
mutagenesis
illumina
long-read
sequencing
2 days ago by
reaset41
• 0
0
votes
0
replies
116
views
GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data
mouse
GATK
Mutect2
dbSNP
2 days ago by
luckyday1661
• 0
0
votes
0
replies
151
views
Bcftools consensus when reference is a deletion
consensus
vcf
3 days ago by
selplat21
▴ 20
0
votes
0
replies
113
views
[maftools]Too many multi_hit and missense mutation
maftools
gatk
MAF
data
WES
VCF
5 days ago by
jiazheng_lin
• 0
0
votes
0
replies
92
views
Extract upstream and downstream 50bp nontemplated sequences from a position
search
sequences
nontemplated
motif
1 day ago by
Ty
• 0
0
votes
0
replies
85
views
How to estimate -g genome-size for Flye for de novo genome or for --meta mode when using Metaflye?
assembly
fasta
genomics
nanopore
pacbio
23 hours ago by
O.rka
▴ 710
1
vote
0
replies
100
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
4 days ago by
joe
▴ 390
0
votes
0
replies
107
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
3 days ago by
rbronste
▴ 420
0
votes
0
replies
34
views
Issue with genetic QC sex check
plink
5 hours ago by
kl
▴ 10
0
votes
0
replies
88
views
ADMIXTURE Freezes Right Before Completion
ADMIXTURE
admixture
1 day ago by
maxlaubstein
• 0
0
votes
0
replies
95
views
how to calculate intramodular connectivity
WGCNA
intramodularConnectivity
1 day ago by
hellokwmin
• 0
0
votes
0
replies
97
views
Conumee output as input for Gistic2.0
cnv
copy
gistic
cna
conumee
updated 2 days ago by
GenoMax
136k • written 2 days ago by
sativus
▴ 10
0
votes
0
replies
106
views
Population study based on metaT and MetaG
metagenome
metatranscriptome
study
population
updated 2 days ago by
GenoMax
136k • written 2 days ago by
PierreGT
• 0
0
votes
0
replies
51
views
How to find promoters (such as GC box and TATA box) in set of genes using bioinformatics analysis ?
motifs
promoters
bioinformatics
5 hours ago by
shome
▴ 10
0
votes
0
replies
40
views
From TPM to raw counts
tpm
Deconvolution
rnaseq
3 hours ago by
Gama313
▴ 120
0
votes
0
replies
33
views
is there a way to set colors pallets for glMDSPlot(x)?
Glimma
glMDSPlot
2 hours ago by
James
• 0
0
votes
0
replies
51
views
Are 10x cellranger-arc ATAC bam files deduplicated?
singlecell
10x
4 hours ago by
WaterMetal
• 0
0
votes
0
replies
82
views
GMT file from eggnog annotation
gmt
annotation
Eggnog
2 days ago by
jorge.cortes.miranda
• 0
3
votes
0
replies
158
views
Herald:
The Biostar Herald for Monday, November 27, 2023
herald
4 days ago by
Biostar
2.3k
0
votes
0
replies
133
views
Job:
Bioinformatican/Data Scientist, Transplant Immunology/Genetics, Medical University of Vienna, Austria
RiskPrediction
NGS
SNP
ExomeSequencing
GeneticRiskScore
1 day ago by
aheinzel
▴ 130
0
votes
0
replies
101
views
Does breadth of coverage signify expression?
Coverage
breadth
Bedtools
Expression
count
3 days ago by
Smriti
▴ 10
0
votes
0
replies
65
views
Osmotic permeability of water transport in aquaporins
permeability
Osmotic
transport
Water
16 hours ago by
Peerzada
• 0
0
votes
0
replies
55
views
Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-voom
RNAseq
differential-gene-expession
limma
batch-effect
4 hours ago by
fluke
• 0
0
votes
0
replies
99
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
4 days ago by
user230613
▴ 350
0
votes
0
replies
126
views
Negative F statistics for sex check in plink
plink
check
sex
5 days ago by
kl
▴ 10
0
votes
0
replies
33
views
Compute matrix skipping many regions stating not found in compute matrix output
computematrix
Deeptools
4 hours ago by
Mehwish
▴ 10
0
votes
0
replies
73
views
Issue softclipping reads when they belong and don't belong to a common amplicon
Samtools
softclip
10 hours ago by
ManuelDB
▴ 80
0
votes
0
replies
107
views
missing region in the process of annotation
annotatr
minfi
3 days ago by
Aki
▴ 10
0
votes
0
replies
334
views
Job:
Postdoctoral Researcher in Alzheimer's disease Genetics, Multi-Omics, and Imaging Biomarkers, St Louis, MO, USA
Multi-Omics
Imaging
Alzheimer
Genetics
3 days ago by
belloy
• 0
0
votes
0
replies
63
views
Significance of several BUSCO target IDs for the same gene
target_id
sequence-ontology
BUSCO
duplication
9 hours ago by
CoLa
• 0
0
votes
0
replies
174
views
Tutorial:
Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation
ggplotify
geom_tile
ggplot2
6 days ago by
rohitsatyam102
▴ 780
0
votes
0
replies
39
views
Job:
Assistant Professor: Molecular Biology
Biology
Molecular
UCSD
3 hours ago by
lta
▴ 10
0
votes
0
replies
90
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
1 day ago by
bioinfo
▴ 140
0
votes
0
replies
106
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
4 days ago by
Jaykishan
• 0
0
votes
0
replies
13
views
Forum:
Low coverage whole genome sequencing reveal excess heterozygosity for multiple SNPs. How to filter?
lcWGS
WGS
heterozygosity
1 hour ago by
beausoleilmo
▴ 560
0
votes
0
replies
74
views
how to download the VCF/MAF files from cBioportal genie site
cBioportal
mutation
VCF
TMB
1 day ago by
luckyday1661
• 0
194 results • Page
4 of 4
Recent Votes
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: GO categorization
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
C: Expected a file with 2 fields per line. GenomicsDBImport from GATK ?
Answer: Problematic fastq files...How can we trust them?
Comment: Problematic fastq files...How can we trust them?
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beausoleilmo
▴ 560
Commentator
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Brian Bushnell
19k
Popular Question
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Gama313
▴ 120
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nanodano
▴ 30
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shome
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Malachi Griffith
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jared.andrews07
★ 16k
Recent Replies
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
by
Brian Bushnell
19k
It's not a silly question! And yes, it can be done. JGI is currently testing various binning tools to try to find the best protocol for t…
Answer: GO categorization
by
geneontologyhelp
▴ 270
[We have this in our FAQ][1]. PANTHER version 18.0, which powers the enrichment analysis on our homepage, has [143 species][2] loaded and …
Comment: Problematic fastq files...How can we trust them?
by
blackadder
▴ 30
Thanks for the feedback fellas! I agree with the aforementioned!
Comment: Which program, tool, or strategy do you use to visualize genomic rearrangements?
by
cmdcolin
★ 3.4k
i collect a large list of tools for visualization, some are specialized for SVs and re-arrangements. you can filter by tag (SV, CNV, compar…
Answer: The number of variations in the pan-genome is reduced compared to the variations
by
Jordan M Eizenga
▴ 410
If variants overlap in the genome, `vg deconstruct` will combine them into one locus with multiple alleles. If your input VCF has a lot of …
Answer: How to find node Postion and source(sample) ?
by
Jordan M Eizenga
▴ 410
You can use `vg find -P` for this. This command is not really designed to be used frequently throughout the genome (each invocation loads t…
Comment: How Can I move the scattered dots more closer into the center of box ?
by
Brian Bushnell
19k
I would just draw them in by hand where you want them.
Comment: How to identify CG, CHG, or CHH from MeDIP data
by
Tm
★ 1.1k
I know that CpG types can be identified using whole genome bisulphite data. But could it be possible using MeDIP data too? We tried using Q…
Comment: Problematic fastq files...How can we trust them?
by
Brian Bushnell
19k
I'd have to agree there... while you can generally recover a fastq to the point that it is spec-compliant, you don't know how or why the f…
Answer: Finding human .vcf files online to download
by
cmdcolin
★ 3.4k
---------- some common ones include 1000 genomes vcf (large, multi-sample) http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/ …
Comment: GO categorization
by
m.habib
• 0
Thanks Istvan for your reply. I think these programs will do the same as Trinotate. Trinotate searches against numerous databases and gener…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
jv
★ 1.2k
I wonder if using cell hashing, which would allow pooling of cells from multiple samples before droplet formation, could improve things her…
Comment: Where Can I Find The Basepair Positions Of Chromosome Bands?
by
Malachi Griffith
19k
And the hg38 version can be found here: https://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/cytoBand.txt.gz And for convenience, upda…
Answer: How Can I move the scattered dots more closer into the center of box ?
by
Trivas
★ 1.5k
You added a position dodge on your boxplot but not on your points.
Comment: How Can I move the scattered dots more closer into the center of box ?
by
ATpoint
78k
Please understand that biostars is not a helpdesk for trivial ggplot questions. Google it and find help on previous StackExchange sites, or…
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