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117,123 results • Page
1 of 2343
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Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
AF
gnomAD
SNP
just now by
liaotsungjen
• 0
0
votes
1
reply
43
views
How to calculate cell type frequency between two groups in single cell data
Seurat
single-cell
sc-RNA
cell-type
updated 24 minutes ago by
Bastien Hervé
5.3k • written 3 hours ago by
Sara
▴ 30
0
votes
0
replies
6
views
Mutation counts corrected by number of samples
mutations
WES
genomics
WGS
20 minutes ago by
garcesj
▴ 50
0
votes
1
reply
2.8k
views
bfctools merge [E::hts_open_format] Failed to open file
SNP
software error
updated 51 minutes ago by
j.f.akers
• 0 • written 3.5 years ago by
andemexoax
• 0
0
votes
1
reply
263
views
LDhat lookup table
LDhat
updated 55 minutes ago by
NÚRIA
• 0 • written 11 months ago by
Matteo
▴ 10
0
votes
0
replies
16
views
BAM to Bedgraph creating an empty file
Bisulfite-seq
bismark
1 hour ago by
irebekah.c
• 0
0
votes
0
replies
19
views
Harmony integration group.by.var parameter
cell
single
harmony
1 hour ago by
Picasa
▴ 640
0
votes
0
replies
27
views
Can you use a polygenic risk score for a trait (e.g., BMI) in association analyses when it doesn't associate with BMI in the sample it is used?
risk
polygenic
score
imputation
2 hours ago by
kl
▴ 10
0
votes
4
replies
92
views
Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
error
Bowtie
updated 2 hours ago by
GenoMax
142k • written 3 hours ago by
Deepthi
• 0
800
votes
167
replies
144k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 4 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
0
votes
1
reply
147
views
Annotating single cell data automatically
cell
annotation
single
updated 3 hours ago by
Francesco
▴ 10 • written 4 weeks ago by
Gerard
• 0
0
votes
2
replies
66
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
1 hour ago by
QX
• 0
1
vote
3
replies
96
views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
subset
updated 1 hour ago by
fracarb8
★ 1.6k • written 4 hours ago by
sc_analysis
• 0
0
votes
1
reply
46
views
Overlapping clusters for different biological conditions: Seurat, UMAP
Seurat
scRNA-seq
UMAP
updated just now by
Bastien Hervé
5.3k • written 4 hours ago by
bio_info
▴ 10
2
votes
4
replies
366
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 3 hours ago by
fracarb8
★ 1.6k • written 7 days ago by
txema.heredia
▴ 130
0
votes
0
replies
47
views
R code for KEGG pathways output
KEGGREST
dplyr
KEGG
R
5 hours ago by
doramora
▴ 10
0
votes
0
replies
37
views
finding highly divergent orthologs using exonerate
ortholog
Exonerate
evolution
6 hours ago by
Emily
▴ 20
2
votes
3
replies
159
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity
mtDNA
PacBio
6 hours ago by
hashim.rana11
▴ 20
0
votes
1
reply
92
views
Does prokka work the same on forward and reverse complementary reads?
Prokka
updated 7 hours ago by
Pierre Lindenbaum
162k • written 8 hours ago by
Maksim
• 0
2
votes
2
replies
123
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
1 hour ago by
F110152169
• 0
8
votes
9
replies
3.0k
views
7 follow
Venter Genome Vcf
vcf
updated 13 hours ago by
ericrkofman
▴ 20 • written 10.1 years ago by
win
▴ 980
0
votes
9
replies
538
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
updated 6 hours ago by
zx8754
11k • written 7 days ago by
hannes.bongartz
• 0
0
votes
0
replies
76
views
16S analysis for specie of bacteria identification
Species-identification
16S
Kraken2
updated 17 hours ago by
Ram
44k • written 17 hours ago by
Christopher
▴ 10
4
votes
1
reply
141
views
PCA plot no distinct cluster. Only p < 0.05 indicates significant DEGs, while adj p < 0.05 does not.
RNA-seq
padj
p-value
updated 18 hours ago by
swbarnes2
14k • written 22 hours ago by
May Ling
• 0
0
votes
0
replies
62
views
abundance_estimates_to_matrix.pl in Trinity is not generating any matrices / output
trinity
updated 18 hours ago by
GenoMax
142k • written 18 hours ago by
jway
• 0
0
votes
3
replies
237
views
What is a good way to do gene differentials in single cell data where one group is small 90 cells and the other group 30,000 cells or 2000 cells.
cell
RNA-Seq
single
updated 16 hours ago by
ATpoint
82k • written 18 hours ago by
shahzaibali
• 0
0
votes
1
reply
121
views
Trying to understand warning from MACS2 about too few paired peaks and differing results in DiffBind
MACS2
ATACseq
DiffBind
updated 18 hours ago by
jared.andrews07
★ 17k • written 22 hours ago by
atan
• 0
0
votes
2
replies
165
views
What do the transcript variant # mean in RefSeq?
refseq
updated 19 hours ago by
Ram
44k • written 22 hours ago by
curious
▴ 750
4
votes
6
replies
335
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
18 hours ago by
Shicheng Guo
★ 9.4k
1
vote
3
replies
233
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 17 hours ago by
Jeremy
▴ 910 • written 1 day ago by
Mohamed Samir
▴ 30
2
votes
0
replies
117
views
Job:
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics
Sequencing
Sweden
Stockholm
SciLifeLab
23 hours ago by
Matthias Zepper
4.6k
0
votes
1
reply
93
views
BEAST2.5 Chloroplast Divergence Time using Fossil Records
BEAST2.5
Fossil
updated 22 hours ago by
Ram
44k • written 23 hours ago by
a.bibek52
▴ 10
3
votes
7
replies
3.9k
views
Difference in Bismark output methylation call files and coverage files
RRBS
Bismark
DNA-methylation
updated 22 hours ago by
Papyrus
★ 2.9k • written 3.9 years ago by
linelr
▴ 40
0
votes
0
replies
108
views
Job:
2 PhD Students in single-cell bioinformatics
PhD
Genomics
single-cell
NGS
6 hours ago by
mtabaka
• 0
0
votes
1
reply
98
views
minfi::getQC - badsamplecutoff 10.5
getqc
minfi
methylation
EPICv2
updated 22 hours ago by
Papyrus
★ 2.9k • written 23 hours ago by
June
• 0
0
votes
2
replies
621
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc
ewas
minfi
updated 23 hours ago by
June
• 0 • written 10 months ago by
rkb965
• 0
2
votes
5
replies
240
views
Z score
Z-score
updated 23 hours ago by
Ram
44k • written 1 day ago by
Akash D
▴ 60
2
votes
6
replies
263
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
7 hours ago by
bio_info
▴ 10
3
votes
3
replies
185
views
Unexpected read length from NGS
NGS
Illumina
5 hours ago by
QX
• 0
0
votes
1
reply
111
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
updated 9 hours ago by
cmdcolin
★ 3.8k • written 1 day ago by
adarsh_pp
▴ 40
1
vote
6
replies
293
views
samtools write-index
samtools
updated 1 day ago by
aw7
▴ 310 • written 2 days ago by
LucisTheFather
• 0
0
votes
2
replies
212
views
How do we do quantification using stringtie merge option for all the merged samples generated.
stringtie
quantification
updated 1 day ago by
i.sudbery
19k • written 2 days ago by
Varsha
• 0
3
votes
2
replies
147
views
How to interpret this plotMDS of three disease clusters?
microarray
plotMDS
DEGs
updated 1 day ago by
ATpoint
82k • written 1 day ago by
egascon
• 0
0
votes
0
replies
72
views
GWAS or QTL mapping in RIL population
GWAS
RIL
1 day ago by
韩雨
• 0
0
votes
0
replies
77
views
VEP annotation tool: "." isn't numeric in addition (+)
VEP
VCF
updated 23 hours ago by
Ram
44k • written 1 day ago by
emmanouil.a
▴ 120
11
votes
13
replies
6.7k
views
7 follow
log2 fold change in RNA-seq analysis
fold
log2
change
updated 23 hours ago by
May Ling
• 0 • written 2.4 years ago by
wmsalsah
▴ 10
0
votes
1
reply
253
views
GWAS Phenotypes
GWAS
updated 1 day ago by
韩雨
• 0 • written 5 weeks ago by
solomoncharles77
▴ 90
5
votes
4
replies
5.1k
views
6 follow
Classic threshold for log2 fold change in RNA-seq experiment
RNA-Seq
updated 1 day ago by
May Ling
• 0 • written 3.9 years ago by
Mozart
▴ 330
1
vote
1
reply
122
views
Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Pooled with Hashtags
5InmuneProfiling
nf-core
scRNAseq
cellranger-multi
Nextflow
updated 1 day ago by
GenoMax
142k • written 1 day ago by
azeu
▴ 10
0
votes
0
replies
59
views
Assigning Micro-C read pairs to nucleosomes called from MNase-seq data?
Hi-C
MNase-Seq
1 day ago by
Linus
• 0
117,123 results • Page
1 of 2343
Recent Votes
Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI
Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
The Biostar Herald for Monday, May 20, 2024
Answer: plink2 cannot make bed file
Answer: plink2 cannot make bed file
Answer: Conda, bioconda, anaconda, are they different?
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Answer: How to calculate cell type frequency between two groups in single cell data
by
Bastien Hervé
5.3k
I believe `sample_id` are your replicates in either `patient` or `control`. You can do it manually by normalizing the number of cells yo…
Answer: bfctools merge [E::hts_open_format] Failed to open file
by
j.f.akers
• 0
I think the program is trying to open a .vcf.gz.csi file rather than the actual data which is the .vcf.gz file, the csi file is not data, j…
Comment: LDhat lookup table
by
NÚRIA
• 0
Hi! Did you manage to fix this? I run convert successfully on 60 unphased diploid samples (1500bp), hence I used lktable available in LDhat…
Comment: Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLI
by
F110152169
• 0
It's Parkinson's disease. How do I get the right order?
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
QX
• 0
yes but they did not reply
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
fracarb8
★ 1.6k
Looking at both `nCount` and `MT` the profile are cut at your thresholds, suggesting that you simply don't have cells with >2000(ish) genes…
Comment: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
Pierre Lindenbaum
162k
did you ask the authors to restore their server ?
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
sc_analysis
• 0
Yes. But after applying: merged_seurat_objects_filtered <- subset(x = merged_seurat_objects, subset = nFeature_RNA > 200 & nFeature_R…
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
by
fracarb8
★ 1.6k
This [paper][1] provides a comparison of the three methods in different settings. [1]: https://genomebiology.biomedcentral.com/articles…
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
Deepthi
• 0
pop up with sam error . Error reading _rstarts[] array: 21720, 23124
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
ATpoint
82k
See me edit I just made for the fastq check.
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
Deepthi
• 0
Thanks will check and update here.
Answer: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
ATpoint
82k
bowtie -x idx file.fastq | samtools view -o out.bam You might be messing up things with these positional arguments. Use this above. Us…
Answer: Annotating single cell data automatically
by
Francesco
▴ 10
- In order to run Azimuth: ``` AzimuthClusters <- RunAzimuth(seurat_obj, reference = "pbmcref") ``` - singleR ``` surveyRefere…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
fracarb8
★ 1.6k
You are not subsetting based on `nFeature`. You are subsetting based on `nFeature` **AND** `nCount` **AND** `perc mt`.
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