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171 results • Page
1 of 4
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Rank
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Votes
Replies
1
vote
10
replies
583
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ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
2 hours ago by
hannes.bongartz
• 0
0
votes
0
replies
51
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
7 hours ago by
marco.barr
▴ 130
0
votes
0
replies
49
views
Duplicates of the same gene in Orthogroup sequence files
orthofinder
9 hours ago by
niconps14
• 0
0
votes
3
replies
171
views
How to scrape BioMart data from https://sorfs.ugent.be/ website
BioMart
updated 9 hours ago by
Pierre Lindenbaum
162k • written 14 hours ago by
QX
• 0
2
votes
3
replies
145
views
Harmony integration group.by.var parameter
single-cell
harmony
updated 6 hours ago by
jared.andrews07
★ 17k • written 12 hours ago by
Picasa
▴ 640
2
votes
1
reply
90
views
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
AF
gnomAD
SNP
updated 9 hours ago by
Jeremy Leipzig
22k • written 10 hours ago by
liaotsungjen
▴ 10
0
votes
0
replies
45
views
Exon Annotation failed using homer annotatePeaks.pl
homer
alternative-splicing
annotatePeaks
updated 9 hours ago by
Ram
44k • written 10 hours ago by
Alessia
• 0
0
votes
2
replies
121
views
How to calculate cell type frequency between two groups in single cell data
Seurat
single-cell
sc-RNA
cell-type
7 hours ago by
Sara
▴ 30
0
votes
1
reply
80
views
Mutation counts corrected by number of samples
mutations
WES
genomics
WGS
updated 9 hours ago by
Ram
44k • written 10 hours ago by
garcesj
▴ 50
0
votes
1
reply
2.9k
views
bfctools merge [E::hts_open_format] Failed to open file
SNP
updated 9 hours ago by
Ram
44k • written 3.6 years ago by
andemexoax
• 0
0
votes
1
reply
311
views
LDhat lookup table
LDhat
updated 9 hours ago by
Ram
44k • written 11 months ago by
Matteo
▴ 10
0
votes
0
replies
55
views
BAM to Bedgraph creating an empty file
Bisulfite-seq
bismark
11 hours ago by
irebekah.c
• 0
0
votes
0
replies
59
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 9 hours ago by
Ram
44k • written 12 hours ago by
kl
▴ 10
0
votes
5
replies
167
views
Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
Bowtie
8 hours ago by
Deepthi
• 0
0
votes
1
reply
174
views
Annotating single cell data automatically
single-cell
updated 9 hours ago by
Ram
44k • written 4 weeks ago by
Gerard
• 0
1
vote
4
replies
215
views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
single-cell
6 hours ago by
sc_analysis
• 0
0
votes
1
reply
117
views
Overlapping clusters for different biological conditions: Seurat, UMAP
Seurat
scRNA-seq
UMAP
updated 10 hours ago by
Bastien Hervé
5.3k • written 14 hours ago by
bio_info
▴ 10
3
votes
4
replies
399
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 13 hours ago by
fracarb8
★ 1.7k • written 8 days ago by
txema.heredia
▴ 130
0
votes
0
replies
82
views
R code for KEGG pathways output
KEGGREST
dplyr
KEGG
R
15 hours ago by
doramora
▴ 10
0
votes
0
replies
55
views
finding highly divergent orthologs using exonerate
ortholog
Exonerate
evolution
16 hours ago by
Emily
▴ 20
2
votes
3
replies
178
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity
mtDNA
PacBio
16 hours ago by
hashim.rana11
▴ 20
0
votes
1
reply
108
views
Does prokka work the same on forward and reverse complementary reads?
Prokka
updated 17 hours ago by
Pierre Lindenbaum
162k • written 18 hours ago by
Maksim
• 0
1
vote
2
replies
191
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
11 hours ago by
F110152169
• 0
8
votes
9
replies
3.1k
views
7 follow
Venter Genome Vcf
vcf
updated 23 hours ago by
ericrkofman
▴ 20 • written 10.1 years ago by
win
▴ 980
0
votes
0
replies
90
views
16S analysis for specie of bacteria identification
Species-identification
16S
Kraken2
updated 1 day ago by
Ram
44k • written 1 day ago by
Christopher
▴ 10
4
votes
1
reply
155
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 1 day ago by
swbarnes2
14k • written 1 day ago by
May Ling
• 0
0
votes
0
replies
75
views
abundance_estimates_to_matrix.pl in Trinity is not generating any matrices / output
trinity
updated 1 day ago by
GenoMax
142k • written 1 day ago by
jway
• 0
0
votes
3
replies
272
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 1 day ago by
ATpoint
82k • written 1 day ago by
shahzaibali
• 0
0
votes
1
reply
134
views
Trying to understand warning from MACS2 about too few paired peaks and differing results in DiffBind
MACS2
ATACseq
DiffBind
updated 1 day ago by
jared.andrews07
★ 17k • written 1 day ago by
atan
• 0
0
votes
2
replies
180
views
What do the transcript variant # mean in RefSeq?
refseq
updated 1 day ago by
Ram
44k • written 1 day ago by
curious
▴ 750
4
votes
6
replies
350
views
Mouse or Rat Gene Expression Data Similar to GTEx
whole-body
expression
atlas
1 day ago by
Shicheng Guo
★ 9.4k
1
vote
3
replies
248
views
Error when looping over multiple columns in a data frame in R
Statistics
R
updated 1 day ago by
Jeremy
▴ 910 • written 2 days ago by
Mohamed Samir
▴ 30
0
votes
1
reply
109
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
1
reply
111
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
633
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
253
views
Z score
Z-score
updated 1 day ago by
Ram
44k • written 1 day ago by
Akash D
▴ 60
2
votes
6
replies
278
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
17 hours ago by
bio_info
▴ 10
3
votes
3
replies
203
views
Unexpected read length from NGS
NGS
Illumina
15 hours ago by
QX
• 0
0
votes
1
reply
125
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
updated 19 hours ago by
cmdcolin
★ 3.8k • written 1 day ago by
adarsh_pp
▴ 40
1
vote
6
replies
306
views
samtools write-index
samtools
updated 1 day ago by
aw7
▴ 310 • written 2 days ago by
LucisTheFather
• 0
0
votes
2
replies
224
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
158
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
83
views
GWAS or QTL mapping in RIL population
GWAS
RIL
1 day ago by
韩雨
• 0
0
votes
0
replies
88
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
264
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
1
vote
1
reply
124
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
171 results • Page
1 of 4
Recent Votes
A: Add contig lenght to VCF header in a robust way
Answer: ComplexHeatmap - How to change fontsize of rowAnnotation
Comment: Harmony integration group.by.var parameter
Answer: Harmony integration group.by.var parameter
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
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Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
GenoMax
142k
> I don't know how widespread these issues are outside of JGI. Very few small/medium sequencing centers likely have NovaSeq X. This is the…
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
Brian Bushnell
20k
Supporting figures, taken from some slides I prepared for internal use. HDist 0, 1, and 2 correspond to 0, 1, and 2 mismatches allowed in …
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
This works. Thank you so so much!
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…
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