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19 results • Page
1 of 1
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Views
Votes
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2
votes
6
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1.9k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 16 hours ago by
Ram
43k • written 2.4 years ago by
SYOSY
▴ 10
4
votes
7
replies
524
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 10 hours ago by
dsull
★ 5.8k • written 4 days ago by
qudrat.nii
▴ 10
4
votes
8
replies
458
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 12 hours ago by
Alex Reynolds
35k • written 1 day ago by
J
▴ 10
3
votes
4
replies
341
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 2 hours ago by
BioinfGuru
★ 1.7k • written 2 days ago by
Ming Tommy Tang
★ 3.9k
1
vote
6
replies
317
views
ScRNA data question
scRNA
Vlnplot
Samples
5 hours ago by
starswillfade
▴ 10
0
votes
5
replies
276
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 1 hour ago by
Istvan Albert
100k • written 3 days ago by
sehriban.buyukkilic
▴ 10
0
votes
3
replies
240
views
Highest variable features in single cell data
single-cell
updated 19 hours ago by
bk11
★ 2.4k • written 2 days ago by
Kazo
• 0
0
votes
0
replies
194
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
18 hours ago by
biocellbio
• 0
0
votes
2
replies
184
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 19 hours ago by
Ram
43k • written 1 day ago by
The_PyPanda
▴ 10
1
vote
2
replies
147
views
gvcf joint calling
WES
GATK
VCF
gVCF
5 hours ago by
zihanss
• 0
0
votes
2
replies
139
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
6 hours ago by
Guille
• 0
2
votes
1
reply
125
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 21 hours ago by
ATpoint
82k • written 21 hours ago by
chaco001
▴ 40
3
votes
0
replies
116
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 19 hours ago by
Ram
43k • written 1 day ago by
Claire Watson
▴ 60
0
votes
1
reply
109
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 12 hours ago by
Gordon Smyth
★ 7.0k • written 1 day ago by
hagl
▴ 10
1
vote
1
reply
106
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
updated 17 hours ago by
Gordon Smyth
★ 7.0k • written 19 hours ago by
pairedttest
▴ 10
0
votes
1
reply
99
views
Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:1.1.1.4, 1.1.1.-, 1.1.1.303)?
ontology
metagenomics
database
enzymes
genomics
updated 9 hours ago by
Mensur Dlakic
★ 27k • written 16 hours ago by
O.rka
▴ 710
0
votes
0
replies
91
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 19 hours ago by
Ram
43k • written 1 day ago by
SineWave
• 0
0
votes
0
replies
89
views
RNA-seq: full length gene
RNA-seq
updated 23 hours ago by
Ram
43k • written 1 day ago by
Nargis
• 0
0
votes
0
replies
75
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 23 hours ago by
Ram
43k • written 1 day ago by
vanbelj
▴ 40
19 results • Page
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Recent Votes
How do I find out the read lenght of a fastq file?
Calculate Allele balance by sample
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
Answer: Is there a tool that sorts gtf files?
Answer: gvcf joint calling
Answer: Heatmap and rna-seq
Answer: How to use limma to find differentially expressed genes in response to a continu
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Popular Question
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rohitsatyam102
▴ 850
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candron
▴ 10
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35k
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Recent Replies
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
Comment: ScRNA data question
by
starswillfade
▴ 10
features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
Comment: gvcf joint calling
by
zihanss
• 0
Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
Comment: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Guille
• 0
Thank you for your answer! The MDS plot seems to group most treatment groups close-by, so I'm starting to suspect the effect of treatment …
Answer: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
Mensur Dlakic
★ 27k
They say that we remember better things we figured out on our own, rather than things we were taught. You were literally two clicks away fr…
Comment: Heatmap and rna-seq
by
dsull
★ 5.8k
https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
Answer: Limma Analysis Agilent Microarray Data (GPL1708)
by
Gordon Smyth
★ 7.0k
There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
Answer: Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
by
Gordon Smyth
★ 7.0k
The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
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 its own contrast. Just run…
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
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
▴ 10
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…
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