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13 results • Page
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0
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11
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How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
22 hours ago by
atowns21
• 0
0
votes
7
replies
293
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 6 hours ago by
GenoMax
141k • written 4 days ago by
Patadu94
• 0
0
votes
3
replies
193
views
Highest variable features in single cell data
single-cell
updated 1 hour ago by
bk11
★ 2.4k • written 1 day ago by
Kazo
• 0
1
vote
2
replies
227
views
PCA plot
DESeq2
PCAplot
updated 13 hours ago by
ATpoint
82k • written 1 day ago by
Aaliya
▴ 10
0
votes
0
replies
48
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 6 hours ago by
Ram
43k • written 6 hours ago by
vanbelj
▴ 40
0
votes
0
replies
64
views
RNA-seq: full length gene
RNA-seq
updated 6 hours ago by
Ram
43k • written 16 hours ago by
Nargis
• 0
0
votes
0
replies
47
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 4 hours ago by
GenoMax
141k • written 7 hours ago by
hagl
▴ 10
0
votes
0
replies
39
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
updated 3 hours ago by
Ram
43k • written 4 hours ago by
Guille
• 0
0
votes
0
replies
63
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 1 hour ago by
Ram
43k • written 16 hours ago by
SineWave
• 0
0
votes
0
replies
24
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
1 hour ago by
biocellbio
• 0
0
votes
0
replies
60
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
18 hours ago by
turcoa1
• 0
1
vote
0
replies
62
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
15 hours ago by
KABILAN
▴ 50
0
votes
0
replies
84
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
13 hours ago by
HarperReed
• 0
13 results • Page
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Recent Votes
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Create a new bed file with all pairwise combinations between two other bed files
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Comment: PCA plot
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Recent Awards •
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Scholar
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Alex Reynolds
35k
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chaco001
▴ 40
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GenoMax
141k
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rheab1230
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bk11
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Answer: How to use limma to find differentially expressed genes in response to a continu
by
Gordon Smyth
★ 7.0k
There's no need for form a contrast because the score variable is already in the model. A continuous variable is it's own contrast. Just ru…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
• 0
Thank you Pierre! I'll try this out with my full data set.
Answer: DNA methylation preprocessing
by
cao510927
▴ 30
I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
Answer: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
Comment: Highest variable features in single cell data
by
bk11
★ 2.4k
You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
Comment: Heatmap and rna-seq
by
GenoMax
141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
by
dsull
★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
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