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32 results • Page
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Tool:
Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvages Failed Runs
NovaDemux
NovaSeq
Illumina
Demultiplexing
Barcode
20 minutes ago by
Brian Bushnell
20k
1
vote
10
replies
585
views
ComplexHeatmap - How to change fontsize of rowAnnotation
r
ComplexHeatmap
3 hours ago by
hannes.bongartz
• 0
0
votes
0
replies
52
views
perl Error - needLargeMem Bigwig
Bigwig
perl
mitosalt
7 hours ago by
marco.barr
▴ 130
0
votes
0
replies
50
views
Duplicates of the same gene in Orthogroup sequence files
orthofinder
9 hours ago by
niconps14
• 0
0
votes
3
replies
172
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
146
views
Harmony integration group.by.var parameter
single-cell
harmony
updated 7 hours ago by
jared.andrews07
★ 17k • written 13 hours ago by
Picasa
▴ 640
2
votes
1
reply
91
views
Why some SNP's allele frequencies in gnomAD are so different between v2 and v4?
AF
gnomAD
SNP
updated 10 hours ago by
Jeremy Leipzig
22k • written 11 hours ago by
liaotsungjen
▴ 10
0
votes
0
replies
46
views
Exon Annotation failed using homer annotatePeaks.pl
homer
alternative-splicing
annotatePeaks
updated 10 hours ago by
Ram
44k • written 11 hours ago by
Alessia
• 0
0
votes
2
replies
122
views
How to calculate cell type frequency between two groups in single cell data
Seurat
single-cell
sc-RNA
cell-type
8 hours ago by
Sara
▴ 30
0
votes
1
reply
81
views
Mutation counts corrected by number of samples
mutations
WES
genomics
WGS
updated 9 hours ago by
Ram
44k • written 11 hours ago by
garcesj
▴ 50
0
votes
1
reply
2.9k
views
bfctools merge [E::hts_open_format] Failed to open file
SNP
updated 10 hours ago by
Ram
44k • written 3.6 years ago by
andemexoax
• 0
0
votes
1
reply
314
views
LDhat lookup table
LDhat
updated 10 hours ago by
Ram
44k • written 11 months ago by
Matteo
▴ 10
0
votes
0
replies
57
views
BAM to Bedgraph creating an empty file
Bisulfite-seq
bismark
12 hours ago by
irebekah.c
• 0
0
votes
0
replies
60
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 10 hours ago by
Ram
44k • written 13 hours ago by
kl
▴ 10
0
votes
5
replies
168
views
Bowtie 1.3.1 alignment error as array 21720,23124 produces sam bam files
Bowtie
9 hours ago by
Deepthi
• 0
0
votes
1
reply
175
views
Annotating single cell data automatically
single-cell
updated 10 hours ago by
Ram
44k • written 4 weeks ago by
Gerard
• 0
1
vote
4
replies
216
views
Single cell analysis: Unable to subset cells in seurat object using desired nFeature_RNA cut off
single-cell
7 hours ago by
sc_analysis
• 0
0
votes
1
reply
118
views
Overlapping clusters for different biological conditions: Seurat, UMAP
Seurat
scRNA-seq
UMAP
updated 11 hours ago by
Bastien Hervé
5.3k • written 15 hours ago by
bio_info
▴ 10
3
votes
4
replies
400
views
Single-cell ambient RNA correction: SoupX vs decontX contamination fraction
single-cell
ambient-RNA
updated 14 hours ago by
fracarb8
★ 1.7k • written 8 days ago by
txema.heredia
▴ 130
0
votes
0
replies
83
views
R code for KEGG pathways output
KEGGREST
dplyr
KEGG
R
16 hours ago by
doramora
▴ 10
0
votes
0
replies
56
views
finding highly divergent orthologs using exonerate
ortholog
Exonerate
evolution
17 hours ago by
Emily
▴ 20
2
votes
3
replies
179
views
How to calculate nucleotide diversity (mtDNA, PacBio_data), Suggest me some tools
NucleotideDiversity
mtDNA
PacBio
17 hours ago by
hashim.rana11
▴ 20
0
votes
1
reply
110
views
Does prokka work the same on forward and reverse complementary reads?
Prokka
updated 18 hours ago by
Pierre Lindenbaum
162k • written 19 hours ago by
Maksim
• 0
1
vote
2
replies
192
views
Trouble with PLINK's logistic regression analysis and covariatesTrouble with PLINK's logistic regression analysis and covariates
PLINK
GWAS
SNP
12 hours ago by
F110152169
• 0
0
votes
0
replies
127
views
Job:
2 PhD Students in single-cell bioinformatics
PhD
Genomics
single-cell
NGS
17 hours ago by
mtabaka
• 0
2
votes
6
replies
280
views
Error with BiocParallel. No barcodes files found
Barcodes
scRNA-seq
SingleCellExperiment
18 hours ago by
bio_info
▴ 10
3
votes
3
replies
204
views
Unexpected read length from NGS
NGS
Illumina
16 hours ago by
QX
• 0
0
votes
1
reply
126
views
Tools for chromosomal aneuploidy detection
genetics
aneuploidy
NGS
human
updated 20 hours ago by
cmdcolin
★ 3.8k • written 1 day ago by
adarsh_pp
▴ 40
1
vote
2
replies
228
views
Construction of circos plot from WGS data
WGS
Circos
19 hours ago by
Anitha
▴ 10
0
votes
3
replies
208
views
Splitting query fasta file for Diamond Blastp make the process faster?
DIAMOND
17 hours ago by
kmat
• 0
0
votes
2
replies
172
views
CreateSeuratObject taking very long
seurat
21 hours ago by
eae6d2e7
• 0
20
votes
17
replies
13k
views
17 follow
Best Practice On Variant Discovery For Bacteria?
updated 17 hours ago by
Ruqaiya
• 0 • written 11.9 years ago by
lh3
33k
32 results • Page
1 of 1
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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Recent Replies
Comment: Introducing NovaDemux, a Sequence Demultiplexer that Increases Yield and Salvage
by
Brian Bushnell
20k
I examined nine 10B runs and five 25B runs (we just started getting 25B flowcells a few months ago). I did not pay close attention but it …
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…
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