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30 results • Page
1 of 1
Sort: replies
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Votes
Replies
8
votes
16
replies
814
views
How to convert plink files to Hapmap Format
GWAS
Plink
updated 11 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 12 hours ago by
cmdcolin
★ 3.8k • written 10.8 years ago by
J.F.Jiang
▴ 920
4
votes
8
replies
377
views
Create a new bed file with all pairwise combinations between two other bed files, based on bp distance
SNPs
BED
eqtl
bedtools
5 hours ago by
J
▴ 10
0
votes
7
replies
303
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 11 hours ago by
GenoMax
141k • written 4 days ago by
Patadu94
• 0
3
votes
6
replies
433
views
7 follow
Heatmap and rna-seq
RNA-Seq
Heatmap
updated 6 hours ago by
GenoMax
141k • written 3 days ago by
qudrat.nii
▴ 10
10
votes
6
replies
9.8k
views
6 follow
CDS vs cDNA vs transcript for mapping RNA-Seq reads
Assembly
rna-seq
alignment
updated 17 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 4 hours ago by
Ram
43k • written 2.3 years ago by
SYOSY
▴ 10
1
vote
5
replies
264
views
ScRNA data question
scRNA
Vlnplot
Samples
updated 12 hours ago by
bk11
★ 2.4k • written 1 day ago by
starswillfade
▴ 10
2
votes
5
replies
282
views
How to trim transcripts using information from NCBI contamination screen report
RNAseq
assembly
transcriptome
contamination
19 hours ago by
Lada
▴ 30
2
votes
3
replies
277
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 8 hours ago by
Ram
43k • written 2 days ago by
Ming Tommy Tang
★ 3.9k
3
votes
3
replies
171
views
genome assembly records not present in assembly_summary.txt
ncbi
bacteria
assembly
updated 15 hours ago by
GenoMax
141k • written 18 hours ago by
sapuizait
▴ 10
0
votes
3
replies
214
views
Highest variable features in single cell data
single-cell
updated 6 hours ago by
bk11
★ 2.4k • written 1 day ago by
Kazo
• 0
2
votes
3
replies
320
views
How to establish haplotype-specific gene expression levels
RNA-seq
Haplotype
updated 14 hours ago by
dsull
★ 5.8k • written 17 days ago by
javanokendo
▴ 60
0
votes
2
replies
169
views
Rare Disease Variant Pathway Analysis
Pathway-analysis
updated 6 hours ago by
Ram
43k • written 1 day ago by
The_PyPanda
▴ 10
2
votes
2
replies
193
views
what is the purpose of indexing the reference genome (Kallisto)
indexing
Kallisto
updated 15 hours ago by
dsull
★ 5.8k • written 22 hours ago by
Aaliya
▴ 10
1
vote
2
replies
238
views
PCA plot
DESeq2
PCAplot
updated 18 hours ago by
ATpoint
82k • written 2 days ago by
Aaliya
▴ 10
1
vote
1
reply
99
views
Source other conda environments in a nextflow pipeline when nextflow itself is in a conda environment?
hpc
conda
nextflow
updated 8 hours ago by
ATpoint
82k • written 9 hours ago by
chaco001
▴ 40
0
votes
1
reply
58
views
Limma Analysis Agilent Microarray Data (GPL1708)
Microarray
Limma
Agilent
updated just now by
Gordon Smyth
★ 7.0k • written 12 hours ago by
hagl
▴ 10
0
votes
1
reply
66
views
Correct way to compare multiple treaments between RNA-Seq samples using edgeR?
RNA-Seq
edgeR
updated 1 hour ago by
Gordon Smyth
★ 7.0k • written 9 hours ago by
Guille
• 0
0
votes
1
reply
76
views
How to use limma to find differentially expressed genes in response to a continuous variable
limma
voom
R
updated 4 hours ago by
Gordon Smyth
★ 7.0k • written 6 hours ago by
pairedttest
▴ 10
0
votes
1
reply
99
views
gvcf joint calling
WES
GATK
VCF
gVCF
updated 23 hours ago by
Jeremy Leipzig
22k • written 23 hours ago by
zihanss
• 0
0
votes
0
replies
71
views
RNA-seq: full length gene
RNA-seq
updated 10 hours ago by
Ram
43k • written 21 hours ago by
Nargis
• 0
1
vote
0
replies
69
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
20 hours ago by
KABILAN
▴ 50
0
votes
0
replies
97
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
18 hours ago by
HarperReed
• 0
0
votes
0
replies
57
views
ChIP-seq datasets: input samples omitted?
ChIP-seq
Normalization
NGS
updated 10 hours ago by
Ram
43k • written 11 hours ago by
vanbelj
▴ 40
0
votes
0
replies
67
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
23 hours ago by
turcoa1
• 0
3
votes
0
replies
99
views
News:
Webinar “Learning Single-cell Atlases” with Dr. Fabian Theis, author of Scanpy on May 8
Scanpy
Generative-AI
scRNA
Machine-Learning
updated 6 hours ago by
Ram
43k • written 17 hours ago by
Claire Watson
▴ 60
0
votes
0
replies
71
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 6 hours ago by
Ram
43k • written 21 hours ago by
SineWave
• 0
0
votes
0
replies
75
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
5 hours ago by
biocellbio
• 0
0
votes
0
replies
31
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
3 hours ago by
O.rka
▴ 710
30 results • Page
1 of 1
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 Awards •
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Scholar
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Alex Reynolds
35k
Popular Question
to
chaco001
▴ 40
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GenoMax
141k
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BioinfGuru
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Recent Replies
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)…
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…
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