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27 results • Page
1 of 1
Sort: replies
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8
votes
16
replies
819
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 15 hours ago by
bk11
★ 2.4k • written 7 weeks ago by
Sofia
• 0
19
votes
11
replies
14k
views
10 follow
How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
utr
updated 16 hours ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
4
votes
8
replies
414
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
updated 3 hours ago by
Alex Reynolds
35k • written 1 day ago by
J
▴ 10
3
votes
7
replies
460
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 1 hour ago by
dsull
★ 5.8k • written 4 days ago by
qudrat.nii
▴ 10
0
votes
7
replies
312
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 15 hours ago by
GenoMax
141k • written 4 days ago by
Patadu94
• 0
10
votes
6
replies
9.8k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 21 hours ago by
Antonio R. Franco
★ 5.1k • written 6.0 years ago by
williamsbrian5064
▴ 510
2
votes
6
replies
1.8k
views
7 follow
DNA methylation preprocessing
SWAN
DNA
methylation
Funnorm
updated 8 hours ago by
Ram
43k • written 2.3 years ago by
SYOSY
▴ 10
2
votes
5
replies
283
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
23 hours ago by
Lada
▴ 30
1
vote
5
replies
274
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 16 hours ago by
bk11
★ 2.4k • written 1 day ago by
starswillfade
▴ 10
0
votes
3
replies
222
views
Highest variable features in single cell data
single-cell
updated 10 hours ago by
bk11
★ 2.4k • written 2 days ago by
Kazo
• 0
3
votes
3
replies
180
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 19 hours ago by
GenoMax
141k • written 23 hours ago by
sapuizait
▴ 10
2
votes
3
replies
321
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 18 hours ago by
dsull
★ 5.8k • written 17 days ago by
javanokendo
▴ 60
2
votes
3
replies
288
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 11 hours ago by
Ram
43k • written 2 days ago by
Ming Tommy Tang
★ 3.9k
1
vote
2
replies
244
views
PCA plot
DESeq2
PCAplot
updated 22 hours ago by
ATpoint
82k • written 2 days ago by
Aaliya
▴ 10
0
votes
2
replies
176
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 10 hours ago by
Ram
43k • written 1 day ago by
The_PyPanda
▴ 10
2
votes
2
replies
204
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 19 hours ago by
dsull
★ 5.8k • written 1 day ago by
Aaliya
▴ 10
0
votes
1
reply
60
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 48 minutes ago by
Mensur Dlakic
★ 27k • written 8 hours ago by
O.rka
▴ 710
1
vote
1
reply
107
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 13 hours ago by
ATpoint
82k • written 13 hours ago by
chaco001
▴ 40
1
vote
1
reply
90
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
updated 8 hours ago by
Gordon Smyth
★ 7.0k • written 10 hours ago by
pairedttest
▴ 10
0
votes
1
reply
85
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
updated 5 hours ago by
Gordon Smyth
★ 7.0k • written 13 hours ago by
Guille
• 0
0
votes
1
reply
88
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated 4 hours ago by
Gordon Smyth
★ 7.0k • written 16 hours ago by
hagl
▴ 10
3
votes
0
replies
106
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 10 hours ago by
Ram
43k • written 21 hours ago by
Claire Watson
▴ 60
0
votes
0
replies
64
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 15 hours ago by
Ram
43k • written 15 hours ago by
vanbelj
▴ 40
0
votes
0
replies
106
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
22 hours ago by
HarperReed
• 0
0
votes
0
replies
79
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 10 hours ago by
Ram
43k • written 1 day ago by
SineWave
• 0
0
votes
0
replies
107
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
10 hours ago by
biocellbio
• 0
0
votes
0
replies
78
views
RNA-seq: full length gene
RNA-seq
updated 15 hours ago by
Ram
43k • written 1 day ago by
Nargis
• 0
27 results • Page
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Recent Votes
A: Blast Settings For Short Sequences
A: Blast Settings For Short Sequences
Comment: Heatmap and rna-seq
Answer: Heatmap and rna-seq
Comment: Heatmap and rna-seq
A: should FASTA files be sorted before indexed with SAMtools?
Answer: A faidx-indexed FASTA format file or a FASTA format file
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Recent Replies
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…
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)…
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