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118,996 results • Page
1 of 2380
Sort: Rank
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Votes
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0
votes
0
replies
43
views
stringdb - where is a description of the database download tables?
stringdb
updated 3 hours ago by
GenoMax
146k • written 4 hours ago by
mcsimenc
▴ 20
0
votes
0
replies
43
views
MS(CSIT) VS MS(DS)
computer-science
career
data-science
updated 3 hours ago by
Ram
44k • written 7 hours ago by
anasjamshed
▴ 140
819
votes
169
replies
155k
views
110 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 16 days ago by
Biostar
3.0k • written 7.8 years ago by
Istvan Albert
101k
0
votes
0
replies
47
views
Strandedness and fetching phyloP scores
python
phyloP
genome
updated 7 hours ago by
Ram
44k • written 7 hours ago by
Yacob
• 0
0
votes
1
reply
55
views
Find SfiI cleavage sites in the human genome
motif
meme
SfiI
fimo
updated 1 hour ago by
GenoMax
146k • written 8 hours ago by
Mitmischer
• 0
0
votes
0
replies
43
views
DMRCate mean diff values
design
methylation
dmrcate
9 hours ago by
Eren
• 0
1
vote
1
reply
176
views
Query about vg (and vg giraffe) for pangenome creation and VC
pangenome
giraffe
vg
updated 1 hour ago by
GenoMax
146k • written 1 day ago by
smriti010305
▴ 10
0
votes
1
reply
74
views
how to get the sample information of 10x genomics datasets of visium HD ?
spatial-transcriptomics
updated 5 hours ago by
GenoMax
146k • written 9 hours ago by
Ibrahim
• 0
1
vote
0
replies
57
views
Inflammatory genes identification
Cancer
inflammatory-genes
RNA-Seq
updated 8 hours ago by
Ram
44k • written 11 hours ago by
Jaber
▴ 20
0
votes
0
replies
62
views
Job:
Postdoctoral Research Fellowship Program at the American Museum of Natural History
Postdoctoral
Research
13 hours ago by
Info-rggs
▴ 20
1
vote
2
replies
128
views
Dealing with 2 different layers of counts within RNA assay in seurat
R
seurat
updated 12 hours ago by
bk11
★ 3.0k • written 14 hours ago by
Varun Gupta
★ 1.3k
0
votes
1
reply
95
views
Understanding IGV
VCF
IGV
BAM
WGS
updated 13 hours ago by
GenoMax
146k • written 14 hours ago by
zizigolu
★ 4.3k
0
votes
2
replies
113
views
Help with subset seurat object by a column in metadata
seurat
8 hours ago by
Chris
▴ 340
7
votes
13
replies
709
views
DESEQ with time series data on mutant vs. wild-type?
DESEQ
updated 13 hours ago by
swbarnes2
14k • written 4 days ago by
Megan
▴ 20
5
votes
9
replies
7.5k
views
GATK "We encountered a non-standard non-IUPAC base in the provided reference: '13"
GATK
updated 14 hours ago by
GenoMax
146k • written 9.0 years ago by
Phismil
▴ 20
0
votes
2
replies
119
views
Bos Taurus, Bos Indicus and Bubalus bubalis GTF,GFF,GFF3 file
and
Buffalo
cattle
updated 11 hours ago by
kalavattam
▴ 270 • written 21 hours ago by
Muhammad
• 0
2
votes
3
replies
188
views
How can I extract 3'UTR of bacteria (Pseudomonas aeruginosa) without using R?
prokaryotes
UTR
updated 8 hours ago by
Ram
44k • written 22 hours ago by
Anshika
• 0
0
votes
2
replies
291
views
vdjtools
vdjtools
updated 21 hours ago by
GenoMax
146k • written 5 months ago by
yueli7
▴ 250
0
votes
0
replies
75
views
Understanding Tumor Contamination vs. Cellularity
Cancer
purity
cnv
23 hours ago by
George
▴ 10
2
votes
1
reply
107
views
Selection Pressure Analysis
Analysis
Evolutionary
PAML
PositiveSelection
updated 22 hours ago by
GenoMax
146k • written 1 day ago by
upasana
▴ 20
1
vote
2
replies
149
views
Using scRNA-seq to draw concrete evidence about transitional cluster
ScRNA-Seq
10 hours ago by
odi
▴ 10
1
vote
3
replies
151
views
MAKER has many FAILED
genome
softmask
MAKER
annotation
updated 2 hours ago by
GenoMax
146k • written 1 day ago by
sansan96
▴ 130
2
votes
1
reply
142
views
Where can I locate cancer genome?
cancer
genome
whole
exome
updated 1 day ago by
GenoMax
146k • written 1 day ago by
Chloe
• 0
0
votes
0
replies
91
views
DiffBind Profile Plot Error
DiffBind
ATAC-seq
updated 1 day ago by
GenoMax
146k • written 1 day ago by
B.N.
▴ 10
2
votes
0
replies
115
views
Tool:
I Built a Simple Website to Help Students Find Research Labs
students
career
research
academia
web-application
1 day ago by
bitsofadventures
▴ 20
0
votes
0
replies
95
views
Bacterial annotators: chromosomes, plasmids, integrons, prophages ?(and other mobile element)
INTEGRONS
CHROMOSOMES
PLASMIDS
updated 1 day ago by
GenoMax
146k • written 1 day ago by
psuazosoto
• 0
8
votes
8
replies
4.1k
views
7 follow
Tool:
New ultraperformant version of SICER/epic: epic2
ChIP-Seq
updated 1 day ago by
GenoMax
146k • written 5.8 years ago by
endrebak852
▴ 110
0
votes
2
replies
163
views
bcftools/vt split multiallelics - split GT along with splitting multi-allelics
multiallelics
decompose
bcftools
vcf
vt
14 hours ago by
Ram
44k
1
vote
4
replies
263
views
VCF filter by read depth
VCF
updated 14 hours ago by
Ram
44k • written 1 day ago by
shu8
• 0
0
votes
0
replies
115
views
Volcano Plot and DGE analysis
DGE
Volcano-Plot
scRNA-seq
updated 1 day ago by
Ram
44k • written 1 day ago by
Ana Sofía
• 0
1
vote
1
reply
148
views
only ~12% of assigned reads on featurecount
RNA-seq
updated 23 hours ago by
DGTool
▴ 250 • written 1 day ago by
diogo.moraes
▴ 20
1
vote
1
reply
182
views
Where can I find a database of healthy genotypes as well as a database of genetic diseases to link these data?
SNPid
database
genotypes
updated 1 day ago by
Jeremy Leipzig
22k • written 1 day ago by
Crypto
▴ 10
2
votes
3
replies
1.8k
views
Weird behaviour - WGCNA hub analysis results in Cytoscape through CytoHubba plugin change every time I run it!
rnaseq
wgcna
cytoscape
hubs
cytohubba
updated 1 day ago by
xanderpico
▴ 580 • written 2.3 years ago by
Raito92
▴ 100
2
votes
5
replies
1.4k
views
UMItools dedup deduplication taking too much time + RAM
UMI-tools
bam
RNA-seq
updated 16 hours ago by
i.sudbery
20k • written 2.7 years ago by
lluc.cabus
▴ 20
0
votes
0
replies
92
views
iMAT (integrative metabolic análisis tool) - MATLAB
iMAT
MATLAB
updated 1 day ago by
Ram
44k • written 1 day ago by
debocolman
• 0
0
votes
1
reply
156
views
Does vg provides an api?
cpp
vg
api
updated 1 day ago by
Jordan M Eizenga
▴ 620 • written 1 day ago by
guntul
▴ 30
1
vote
2
replies
175
views
Aligning a genome with a size of about 300,000.
Alignment
snapgen
genome
updated 1 day ago by
GenoMax
146k • written 1 day ago by
trezini
• 0
0
votes
0
replies
101
views
Similar tools to visualize pileup of long-read alignments to a STR locus
str
long-reads
pileups
nanopore
1 day ago by
Antonio
• 0
2
votes
1
reply
146
views
What is trait discoverability?
snp
phenotype
gene
trait
updated 1 day ago by
GenoMax
146k • written 1 day ago by
_quantum_girl_
▴ 60
0
votes
0
replies
109
views
Salmon transcript-level to gene-level quantification
R
Salmon
RNA-Seq
1 day ago by
Mitmischer
• 0
1
vote
1
reply
149
views
SNP Density plot with custom genome using karyoploteR
NGS
SNP
R
updated 1 day ago by
zx8754
12k • written 1 day ago by
adarsh_munna
▴ 50
1
vote
2
replies
189
views
Need help with AUGUSTUS and AGAT for gene prediction and feature extraction, respectively.
augustus
AGAT
annotation
genome
agat
1 day ago by
Vijith
▴ 40
0
votes
3
replies
213
views
Detection of unknown sub cells in a population of cells using DEGs from scRNAseq data
scRNAseq
updated 22 hours ago by
ATpoint
84k • written 1 day ago by
ashkan
▴ 160
3
votes
5
replies
417
views
Decision on Upregulated/Downregulated Genes in DE list- P-value and Log fold change
Pvalue
logfoldchange
updated 7 hours ago by
Mensur Dlakic
★ 28k • written 2 days ago by
odi
▴ 10
6
votes
24
replies
1.0k
views
TCGA Biolinks code issue
normalization
TCGAbiolinks
updated 1 day ago by
mazegriff
▴ 70 • written 3 days ago by
nuorain
▴ 20
0
votes
3
replies
345
views
Error in pheatmap 'Error in hclust(d, method = method) : must have n >= 2 objects to cluster' for selected genes
pheatmap
updated 2 days ago by
Mensur Dlakic
★ 28k • written 2 days ago by
aackermann287
• 0
0
votes
5
replies
285
views
MarkDuplicatesSpark throwing disk quota errors
GATK
1 day ago by
ChumBucket2024
• 0
0
votes
0
replies
120
views
Linear Mixed-effects Modelling for Mouse Tumor Growth Data
lmerTest
modelling
mixed-effects
lme4
2 days ago by
BioNovice247
▴ 20
3
votes
4
replies
329
views
Cannot process a custom VCF file using bcftools
R
bcftools
VCF
updated 2 days ago by
Pierre Lindenbaum
164k • written 3 days ago by
Qiong
▴ 10
0
votes
1
reply
164
views
filter genes for differential gene expression
RNA-seq
differential-gene-expression
updated 2 days ago by
Ram
44k • written 2 days ago by
bleven
• 0
118,996 results • Page
1 of 2380
Recent Votes
Comment: MAKER has many FAILED
C: HISAT2 V.S. STAR
Inflammatory genes identification
Answer: Identify SNPs with Fst estimates > 0.9 and annotate them
Comment: Where can I locate cancer genome?
Answer: The Evolution of NGS: What’s New and What’s Next?
The Evolution of NGS: What’s New and What’s Next?
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Recent Awards •
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Popular Question
to
yang.zhizhang
▴ 10
Teacher
to
GenoMax
146k
Popular Question
to
anasjamshed
▴ 140
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to
dec986
▴ 380
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zizigolu
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Recent Replies
Comment: Find SfiI cleavage sites in the human genome
by
GenoMax
146k
> As from understanding, either a site matches a motif or it doesn't. To add another wrinkle, [**NEB is listing this enzyme**][1] as one …
Comment: MAKER has many FAILED
by
GenoMax
146k
This may sound stupid but let us go in the other direction. Have the contigs been filtered and QC'ed (for minimum length/content e.g. no po…
Comment: MAKER has many FAILED
by
sansan96
▴ 130
Hi @genomax It finishes but does not throw any error, I even increased the ram memory but I still have no success, do you recommend anoth…
Comment: how to get the sample information of 10x genomics datasets of visium HD ?
by
GenoMax
146k
Please do not ask similar question in different threads: https://www.biostars.org/p/9603180/ You can also follow up on individual papers (…
Comment: Decision on Upregulated/Downregulated Genes in DE list- P-value and Log fold cha
by
Mensur Dlakic
★ 28k
My main point was that instead of `you can set threshold where you think is reasonable` it should be `you can set threshold where you think…
Comment: Help with subset seurat object by a column in metadata
by
Chris
▴ 340
Thank you for your reply! Unfortunately, I got the same error message.
Comment: What is a read group?
by
dylanmontanamarshall
• 0
thank you for clarifying!
Answer: Query about vg (and vg giraffe) for pangenome creation and VC
by
Jouni Sirén
▴ 420
Manual index construction is mostly for developers and early adopters these days, and every step in it is full of pitfalls. Once we have es…
Comment: Using scRNA-seq to draw concrete evidence about transitional cluster
by
odi
▴ 10
Thank you for your response. I definitely plan to use trajectory/pseudotime analysis and maybe make some diffusion map plots. But the spati…
Comment: Dealing with 2 different layers of counts within RNA assay in seurat
by
Varun Gupta
★ 1.3k
Thanks!!! This worked obj_seurat[["RNA"]]$`counts.Antibody Capture` <- NULL
Comment: Help with subset seurat object by a column in metadata
by
bk11
★ 3.0k
If `sample` is one of the column in `meta.data`, you can subset sample "1" using following commands: Idents(combined_seurat_large) <- …
Answer: Dealing with 2 different layers of counts within RNA assay in seurat
by
bk11
★ 3.0k
Please do check how you can remove a layer or subset of layer from a Seurat Object in the following link: [Seurat v5 Command Cheat Sheet][…
Comment: DESEQ with time series data on mutant vs. wild-type?
by
swbarnes2
14k
Yes, if you want to compare one subgroup to a second subgroup, do it this way. You can make the same comparison with the interaction desig…
Comment: Proxy Variant SNP for PRS
by
Sam
★ 4.8k
Have you tried performing imputation on your target data?
Comment: DESEQ with time series data on mutant vs. wild-type?
by
Megan
▴ 20
Here is an updated photo. I was given this data from my PI, where there were three biological replicates each for the samples. I had to rem…
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