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186 results • Page
1 of 4
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Votes
Replies
0
votes
0
replies
18
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
1 hour ago by
marco.barr
▴ 130
0
votes
0
replies
25
views
Duplicates of the same gene in Orthogroup sequence files
orthofinder
2 hours ago by
niconps14
• 0
0
votes
3
replies
133
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 3 hours ago by
Pierre Lindenbaum
162k • written 7 hours ago by
QX
• 0
0
votes
3
replies
76
views
Harmony integration group.by.var parameter
single-cell
harmony
updated 30 minutes ago by
jared.andrews07
★ 17k • written 6 hours ago by
Picasa
▴ 640
2
votes
1
reply
60
views
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
AF
gnomAD
SNP
updated 3 hours ago by
Jeremy Leipzig
22k • written 4 hours ago by
liaotsungjen
▴ 10
0
votes
0
replies
26
views
Exon Annotation failed using homer annotatePeaks.pl
homer
alternative-splicing
annotatePeaks
updated 3 hours ago by
Ram
44k • written 4 hours ago by
Alessia
• 0
0
votes
2
replies
81
views
How to calculate cell type frequency between two groups in single cell data
Seurat
single-cell
sc-RNA
cell-type
1 hour ago by
Sara
▴ 30
0
votes
1
reply
50
views
Mutation counts corrected by number of samples
mutations
WES
genomics
WGS
updated 3 hours ago by
Ram
44k • written 4 hours ago by
garcesj
▴ 50
0
votes
1
reply
2.9k
views
bfctools merge [E::hts_open_format] Failed to open file
SNP
updated 3 hours ago by
Ram
44k • written 3.6 years ago by
andemexoax
• 0
0
votes
1
reply
289
views
LDhat lookup table
LDhat
updated 3 hours ago by
Ram
44k • written 11 months ago by
Matteo
▴ 10
0
votes
0
replies
35
views
BAM to Bedgraph creating an empty file
Bisulfite-seq
bismark
5 hours ago by
irebekah.c
• 0
0
votes
0
replies
49
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?
polygenic-risk-score
imputation
updated 3 hours ago by
Ram
44k • written 6 hours ago by
kl
▴ 10
0
votes
5
replies
143
views
Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
Bowtie
2 hours ago by
Deepthi
• 0
0
votes
1
reply
164
views
Annotating single cell data automatically
single-cell
updated 3 hours ago by
Ram
44k • written 4 weeks ago by
Gerard
• 0
1
vote
4
replies
151
views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
single-cell
54 minutes ago by
sc_analysis
• 0
0
votes
1
reply
84
views
Overlapping clusters for different biological conditions: Seurat, UMAP
Seurat
scRNA-seq
UMAP
updated 4 hours ago by
Bastien Hervé
5.3k • written 8 hours ago by
bio_info
▴ 10
3
votes
4
replies
384
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 7 hours ago by
fracarb8
★ 1.7k • written 8 days ago by
txema.heredia
▴ 130
0
votes
0
replies
71
views
R code for KEGG pathways output
KEGGREST
dplyr
KEGG
R
9 hours ago by
doramora
▴ 10
0
votes
0
replies
45
views
finding highly divergent orthologs using exonerate
ortholog
Exonerate
evolution
10 hours ago by
Emily
▴ 20
2
votes
3
replies
168
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity
mtDNA
PacBio
10 hours ago by
hashim.rana11
▴ 20
0
votes
1
reply
98
views
Does prokka work the same on forward and reverse complementary reads?
Prokka
updated 11 hours ago by
Pierre Lindenbaum
162k • written 12 hours ago by
Maksim
• 0
1
vote
2
replies
170
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
5 hours ago by
F110152169
• 0
8
votes
9
replies
3.1k
views
7 follow
Venter Genome Vcf
vcf
updated 17 hours ago by
ericrkofman
▴ 20 • written 10.1 years ago by
win
▴ 980
0
votes
9
replies
545
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
updated 11 hours ago by
zx8754
11k • written 7 days ago by
hannes.bongartz
• 0
0
votes
0
replies
82
views
16S analysis for specie of bacteria identification
Species-identification
16S
Kraken2
updated 21 hours ago by
Ram
44k • written 22 hours ago by
Christopher
▴ 10
4
votes
1
reply
148
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 22 hours ago by
swbarnes2
14k • written 1 day ago by
May Ling
• 0
0
votes
0
replies
66
views
abundance_estimates_to_matrix.pl in Trinity is not generating any matrices / output
trinity
updated 22 hours ago by
GenoMax
142k • written 22 hours ago by
jway
• 0
0
votes
3
replies
254
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 20 hours ago by
ATpoint
82k • written 22 hours ago by
shahzaibali
• 0
0
votes
1
reply
126
views
Trying to understand warning from MACS2 about too few paired peaks and differing results in DiffBind
MACS2
ATACseq
DiffBind
updated 23 hours ago by
jared.andrews07
★ 17k • written 1 day ago by
atan
• 0
0
votes
2
replies
170
views
What do the transcript variant # mean in RefSeq?
refseq
updated 23 hours ago by
Ram
44k • written 1 day ago by
curious
▴ 750
4
votes
6
replies
340
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
23 hours ago by
Shicheng Guo
★ 9.4k
1
vote
3
replies
239
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 22 hours ago by
Jeremy
▴ 910 • written 1 day ago by
Mohamed Samir
▴ 30
2
votes
0
replies
123
views
Job:
Permanent Position as Researcher/Computational Biologist at the National Genomics Infrastructure (Sweden)
Genomics
Sequencing
Sweden
Stockholm
SciLifeLab
1 day ago by
Matthias Zepper
4.6k
0
votes
1
reply
100
views
BEAST2.5 Chloroplast Divergence Time using Fossil Records
BEAST2.5
Fossil
updated 1 day ago by
Ram
44k • written 1 day 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 1 day ago by
Papyrus
★ 2.9k • written 3.9 years ago by
linelr
▴ 40
0
votes
0
replies
117
views
Job:
2 PhD Students in single-cell bioinformatics
PhD
Genomics
single-cell
NGS
11 hours ago by
mtabaka
• 0
0
votes
1
reply
103
views
minfi::getQC - badsamplecutoff 10.5
getqc
minfi
methylation
EPICv2
updated 1 day ago by
Papyrus
★ 2.9k • written 1 day ago by
June
• 0
0
votes
2
replies
625
views
minfi::getQC - is default badsamplecutoff of 10.5 always appropriate? ~half of samples fail by this measure
getqc
ewas
minfi
updated 1 day ago by
June
• 0 • written 10 months ago by
rkb965
• 0
2
votes
5
replies
244
views
Z score
Z-score
updated 1 day ago by
Ram
44k • written 1 day ago by
Akash D
▴ 60
2
votes
6
replies
270
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
11 hours ago by
bio_info
▴ 10
3
votes
3
replies
194
views
Unexpected read length from NGS
NGS
Illumina
9 hours ago by
QX
• 0
0
votes
1
reply
117
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
updated 13 hours ago by
cmdcolin
★ 3.8k • written 1 day ago by
adarsh_pp
▴ 40
1
vote
6
replies
298
views
samtools write-index
samtools
updated 1 day ago by
aw7
▴ 310 • written 2 days ago by
LucisTheFather
• 0
0
votes
2
replies
217
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
151
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
76
views
GWAS or QTL mapping in RIL population
GWAS
RIL
1 day ago by
韩雨
• 0
0
votes
0
replies
81
views
VEP annotation tool: "." isn't numeric in addition (+)
VEP
VCF
updated 1 day 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 1 day ago by
May Ling
• 0 • written 2.4 years ago by
wmsalsah
▴ 10
0
votes
1
reply
257
views
GWAS Phenotypes
GWAS
updated 1 day ago by
韩雨
• 0 • written 5 weeks ago by
solomoncharles77
▴ 90
5
votes
4
replies
5.2k
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
186 results • Page
1 of 4
Recent Votes
A: Blast - Formatting Output
Answer: Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
Comment: Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
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
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Recent Replies
Comment: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
>I am not sure, but using "Sample_ID" might remove the differences between the conditions right ? More than likely, it'd at least impact t…
Comment: Harmony integration group.by.var parameter
by
Picasa
▴ 640
Thanks jared.andrews07 for your answer. So, you are suggesting to use only "Donor" in the integration? ```r RunHarmony(seu_obj, group.by.…
Comment: Single cell analysis: Unable to subset cells in seurat object using desired nFea
by
sc_analysis
• 0
I am not sure what should be the cut off. Looking at the vlnplot before subsetting i thought most of the cells are falling under 7500 nfeat…
Comment: How to calculate cell type frequency between two groups in single cell data
by
Sara
▴ 30
Thank you for your comment and sorry if this question might be so basic. How can I normalize the number of cells? If I am not wrong the i…
Comment: Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
by
Deepthi
• 0
I unzipped the fastq files to check whether reads are trimmed adapter or not. I have checked the quality control using fastqc they are go…
Comment: Mutation counts corrected by number of samples
by
Ram
44k
> I want to compare the number of mutations This comparison will give you literally no useful information.
Answer: How to scrape BioMart data from https://sorfs.ugent.be/ website
by
Pierre Lindenbaum
162k
something like: seq 1 100 4377380 | while read F ; do wget --no-check-certificate -O - "https://sorfs.ugent.be/database/micrope…
Answer: Harmony integration group.by.var parameter
by
jared.andrews07
★ 17k
The variability explained by the variables provided to `group.by.vars` is what Harmony will try to remove. Assuming you want to remove the …
Answer: Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
by
Jeremy Leipzig
22k
That SNP is in an HLA gene which has had a lot of attention and improvement over the years, ranging from kits to software to the reference …
Comment: Overlapping clusters for different biological conditions: Seurat, UMAP
by
Bastien Hervé
5.3k
What is the need of PBMC in your analysis ? If none, removing them from the beginning will allow your clusters to be more specific to your …
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 LDh…
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
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