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118,989 results • Page
1 of 2380
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Job:
Postdoctoral Research Fellowship Program at the American Museum of Natural History
Postdoctoral
Research
41 minutes ago by
Info-rggs
▴ 20
0
votes
1
reply
21
views
Dealing with 2 different layers of counts within RNA assay in seurat
R
seurat
updated just now by
bk11
★ 3.0k • written 1 hour ago by
Varun Gupta
★ 1.3k
0
votes
1
reply
33
views
Understanding IGV
VCF
IGV
BAM
WGS
updated 1 hour ago by
GenoMax
146k • written 2 hours ago by
zizigolu
★ 4.3k
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
1
reply
25
views
Help with subset seurat object by a column in metadata
seurat
updated just now by
bk11
★ 3.0k • written 2 hours ago by
Chris
▴ 340
7
votes
13
replies
627
views
DESEQ with time series data on mutant vs. wild-type?
DESEQ
updated 43 minutes 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 2 hours ago by
GenoMax
146k • written 9.0 years ago by
Phismil
▴ 20
0
votes
2
replies
91
views
Bos Taurus, Bos Indicus and Bubalus bubalis GTF,GFF,GFF3 file
and
Buffalo
cattle
updated 5 hours ago by
kalavattam
▴ 270 • written 8 hours ago by
Muhammad
• 0
2
votes
3
replies
155
views
How can I extract 3'UTR of bacteria (Pseudomonas aeruginosa) without using R?
prokaryotes
bioinformatics
UTR
gene
updated 4 hours ago by
Michael
55k • written 10 hours ago by
Anshika
• 0
0
votes
2
replies
273
views
vdjtools
vdjtools
updated 8 hours ago by
GenoMax
146k • written 5 months ago by
yueli7
▴ 250
0
votes
0
replies
53
views
Understanding Tumor Contamination vs. Cellularity
Cancer
purity
cnv
11 hours ago by
George
▴ 10
2
votes
1
reply
81
views
Selection Pressure Analysis
Analysis
Evolutionary
PAML
PositiveSelection
updated 9 hours ago by
GenoMax
146k • written 11 hours ago by
upasana
▴ 20
0
votes
1
reply
100
views
Using scRNA-seq to draw concrete evidence about transitional cluster
ScRNA-Seq
updated 12 hours ago by
yura.grabovska
▴ 430 • written 16 hours ago by
odi
▴ 10
0
votes
1
reply
91
views
MAKER has many FAILED
genome
softmask
MAKER
annotation
updated 12 hours ago by
GenoMax
146k • written 12 hours ago by
sansan96
▴ 130
1
vote
1
reply
114
views
Where can I locate cancer genome?
cancer
genome
whole
exome
updated 13 hours ago by
GenoMax
146k • written 17 hours ago by
Chloe
• 0
0
votes
0
replies
68
views
DiffBind Profile Plot Error
DiffBind
ATAC-seq
updated 13 hours ago by
GenoMax
146k • written 17 hours ago by
B.N.
▴ 10
2
votes
0
replies
94
views
Tool:
I Built a Simple Website to Help Students Find Research Labs
students
career
research
academia
web-application
18 hours ago by
bitsofadventures
▴ 20
0
votes
0
replies
76
views
Bacterial annotators: chromosomes, plasmids, integrons, prophages ?(and other mobile element)
INTEGRONS
CHROMOSOMES
PLASMIDS
updated 16 hours ago by
GenoMax
146k • written 19 hours ago by
psuazosoto
• 0
8
votes
8
replies
4.1k
views
7 follow
Tool:
New ultraperformant version of SICER/epic: epic2
ChIP-Seq
updated 16 hours ago by
GenoMax
146k • written 5.8 years ago by
endrebak852
▴ 110
0
votes
2
replies
119
views
bcftools/vt split multiallelics - split GT along with splitting multi-allelics
multiallelics
decompose
bcftools
vcf
vt
1 hour ago by
Ram
44k
1
vote
4
replies
209
views
VCF filter by read depth
VCF
updated 1 hour ago by
Ram
44k • written 22 hours ago by
shu8
• 0
0
votes
0
replies
96
views
Volcano Plot and DGE analysis
DGE
Volcano-Plot
scRNA-seq
updated 21 hours ago by
Ram
44k • written 23 hours ago by
Ana Sofía
• 0
1
vote
1
reply
122
views
only ~12% of assigned reads on featurecount
RNA-seq
updated 11 hours ago by
DGTool
▴ 250 • written 1 day ago by
diogo.moraes
▴ 20
1
vote
1
reply
161
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 4 hours ago by
i.sudbery
20k • written 2.7 years ago by
lluc.cabus
▴ 20
0
votes
0
replies
73
views
iMAT (integrative metabolic análisis tool) - MATLAB
iMAT
MATLAB
updated 21 hours ago by
Ram
44k • written 1 day ago by
debocolman
• 0
0
votes
1
reply
137
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
151
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
84
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
127
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
92
views
Salmon transcript-level to gene-level quantification
R
Salmon
RNA-Seq
1 day ago by
Mitmischer
• 0
1
vote
1
reply
131
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
170
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
191
views
Detection of unknown sub cells in a population of cells using DEGs from scRNAseq data
scRNAseq
updated 10 hours ago by
ATpoint
84k • written 1 day ago by
ashkan
▴ 160
1
vote
0
replies
116
views
Query about vg (and vg giraffe) for pangenome creation and VC
vg
pangenome
giraffe
1 day ago by
smriti010305
▴ 10
2
votes
4
replies
346
views
Decision on Upregulated/Downregulated Genes in DE list- P-value and Log fold change
Pvalue
logfoldchange
updated 4 hours ago by
i.sudbery
20k • written 1 day ago by
odi
▴ 10
6
votes
24
replies
967
views
TCGA Biolinks code issue
normalization
TCGAbiolinks
updated 20 hours ago by
mazegriff
▴ 70 • written 2 days ago by
nuorain
▴ 20
0
votes
3
replies
312
views
Error in pheatmap 'Error in hclust(d, method = method) : must have n >= 2 objects to cluster' for selected genes
pheatmap
updated 1 day ago by
Mensur Dlakic
★ 28k • written 1 day ago by
aackermann287
• 0
0
votes
5
replies
262
views
MarkDuplicatesSpark throwing disk quota errors
GATK
1 day ago by
ChumBucket2024
• 0
0
votes
0
replies
102
views
Linear Mixed-effects Modelling for Mouse Tumor Growth Data
lmerTest
modelling
mixed-effects
lme4
1 day ago by
BioNovice247
▴ 20
3
votes
4
replies
303
views
Cannot process a custom VCF file using bcftools
R
bcftools
VCF
updated 1 day ago by
Pierre Lindenbaum
164k • written 2 days ago by
Qiong
▴ 10
0
votes
1
reply
145
views
filter genes for differential gene expression
RNA-seq
differential-gene-expression
updated 1 day ago by
Ram
44k • written 2 days ago by
bleven
• 0
0
votes
0
replies
119
views
Best Practices for Tumor-Only WES Data Analysis: Seeking Feedback on Variant Calling Pipeline
GATK
Mutect
WES
Cancer
2 days ago by
George
▴ 10
0
votes
0
replies
102
views
CODEX/Phenocycler -> QuPath -> Seurat pipeline basic help needed
QuPath
CODEX
Seurat
Phenocycler
2 days ago by
yura.grabovska
▴ 430
0
votes
1
reply
191
views
How to compare SNPs in different population
SNPs
genome
VCF
updated 2 days ago by
dthorbur
★ 2.5k • written 3 days ago by
Elisa
• 0
0
votes
0
replies
100
views
News:
RADseq data analysis using Stacks (online course)
RADseq
Phylogenomics
Population-Genomics
Stacks
updated 2 days ago by
Ram
44k • written 2 days ago by
carlopecoraro2
★ 2.6k
0
votes
2
replies
153
views
KEGG MAPPER Reconstruct
KEGG
MAPPER
updated 2 days ago by
andres.firrincieli
3.7k • written 2 days ago by
Julián
• 0
6
votes
6
replies
296
views
RNA-Seq multiple lane
bam
RNA-seq
transcriptomics
1 day ago by
MaxMin
▴ 10
1
vote
4
replies
218
views
Problems with Megahit wanting to overwrite the Input for the output directory
metagenomics
megahit
slurm
updated 2 days ago by
Pierre Lindenbaum
164k • written 2 days ago by
Jan
• 0
118,989 results • Page
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Recent Votes
Answer: UK biobank versus Genomics England
Answer: tfea.chip mouse server
I Built a Simple Website to Help Students Find Research Labs
Answer: How can I extract 3'UTR of bacteria (Pseudomonas aeruginosa) without using R?
How to determine assembly of a VCF?
Can Illumina bcl2fastq use only one index for demultiplexing dual index sequencing data?
Comment: How can I extract 3'UTR of bacteria (Pseudomonas aeruginosa) without using R?
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Info-rggs
▴ 20
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zizigolu
★ 4.3k
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to
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▴ 340
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upasana
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Recent Replies
Comment: 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…
Comment: DESEQ with time series data on mutant vs. wild-type?
by
swbarnes2
14k
You should add condition to this plot. If the subclusters match with condition, this isn't so bad. Though only 10 samples? 5 v 5 would h…
Comment: Understanding IGV
by
GenoMax
146k
Why are there more than one screenshot if you are referring to a specific location? Which of the shots is supposed to be the location (you …
Comment: HTseq count issue, not aligning to features
by
boone5jones
• 0
Thank you for your help. I appreciate it.
Comment: bcftools/vt split multiallelics - split GT along with splitting multi-allelics
by
Ram
44k
You're absolutely right - I lost sight of that. I'm working with cancer cells, so polyploidy is a possibility. Is there any way to address…
Comment: VCF filter by read depth
by
Ram
44k
It's no inconvenience, I was just clarifying what your goal is here. You can use `bcftools view` to filter using read-depth. You should use…
Comment: GATK "We encountered a non-standard non-IUPAC base in the provided reference: '1
by
GenoMax
146k
Click here --> https://www.biostars.org/p/162747/#162748
Comment: Combining GSEA (Gene Set Enrichment analysis) and DEG (Differentially Expressed
by
arnaud_p
• 0
Hi old toppic, but I think the question is still of interest. I'm used to working with RNAseq data, mainly from mouse liver. Based on my ex…
Answer: DESEQ with time series data on mutant vs. wild-type?
by
Megan
▴ 20
It looks like there was an issue with the colData, where the KO was labeled as the WT instead. I corrected it and the fmr1 account is corre…
Answer: DESEQ with time series data on mutant vs. wild-type?
by
Megan
▴ 20
Hi Maze, I had to use this account to response to you. Sorry about that. I made a PCA plot with both samples and this is what I got. I …
Comment: GATK "We encountered a non-standard non-IUPAC base in the provided reference: '1
by
skdv2522
• 0
which command you are talking about
Comment: GATK "We encountered a non-standard non-IUPAC base in the provided reference: '1
by
skdv2522
• 0
9:42:57.242 INFO PairHMM - Total compute time in PairHMM computeLogLikelihoods() : 0.0 19:42:57.242 INFO SmithWatermanAligner - Total co…
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