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1,000 results • Page
3 of 20
Sort: Votes
Rank
Views
Votes
Replies
4
votes
5
replies
779
views
Does adding reads cause batch effects?
kallisto
RNAseq
10 months ago by
bioinfo
▴ 150
4
votes
4
replies
645
views
Feedback on mouse brain scRNA-seq quality control
mouse
brain
singe-cell
scRNAseq
quality-control
8 months ago by
nshenoy
▴ 50
4
votes
3
replies
588
views
Over Representation analysis altered pathways in common between comparisons plot
R
Visualization
DGE
ORA
updated 6 months ago by
Basti
★ 2.0k • written 6 months ago by
Manuel
▴ 10
4
votes
6
replies
1.8k
views
Failure in installing the ggtree, enrichplot, and ggtree (Bioconductor packages )
Bioconductor
updated 9 months ago by
GenoMax
141k • written 9 months ago by
applepie
• 0
4
votes
14
replies
2.7k
views
Is it possible to annotate single genes by snpeff
snp
vcf
updated 10 months ago by
Ram
43k • written 6.7 years ago by
misbahabas
▴ 70
4
votes
3
replies
586
views
Identifying enhancers that regulate certain genes
enhancers
updated 9 months ago by
rfran010
▴ 900 • written 9 months ago by
Rozita
▴ 40
4
votes
8
replies
3.5k
views
How to reduce the number of SNPs for the Lositan software
Lositan
SNP
updated 10 months ago by
Ram
43k • written 9.5 years ago by
zhaojianli198322
• 0
4
votes
1
reply
624
views
How to interpret Clustree results?
scRNA
clustering
clustree
updated 8 months ago by
LChart
3.9k • written 8 months ago by
leranwangcs
▴ 120
4
votes
3
replies
745
views
BBduk log and stats appear to be inconsistent
bbduk
bbmap
updated 11 months ago by
GenoMax
141k • written 11 months ago by
Dave Carlson
★ 1.7k
4
votes
8
replies
1.8k
views
Error while running nf-core/rnaseq pipeline
nf-core
RNA-seq
11 months ago by
eesha28112001
• 0
4
votes
9
replies
572
views
variant calling
variant-calling
updated 23 days ago by
Ram
43k • written 24 days ago by
dalibenam64
• 0
4
votes
7
replies
1.4k
views
.bed files from sequencing platform not containing intervals of "alt", "random" haplotypes. How do I perform coverage and haplotype caller?
exome
.bed
haplotypes
HG38
coverage
updated 9 months ago by
GenoMax
141k • written 9 months ago by
LeandroF.
• 0
4
votes
4
replies
605
views
Request for a linkage analysis tutorial
linkage
updated 8 months ago by
GenoMax
141k • written 8 months ago by
German.M.Demidov
★ 2.9k
4
votes
6
replies
2.1k
views
Single nucleotide Polymorphism (SNP)
SNP
updated 10 months ago by
Ram
43k • written 9.0 years ago by
Harish Sanja
▴ 10
4
votes
5
replies
1.1k
views
STAR mapping - regarding output files content
STAR
RNA-seq
mapping
updated 8 months ago by
rfran010
▴ 900 • written 8 months ago by
Manko47
• 0
4
votes
7
replies
1.0k
views
Statistical test to compare data across timepoints
Statistics
updated 6 months ago by
Matthias Zepper
4.5k • written 6 months ago by
Sean
▴ 20
4
votes
6
replies
1.1k
views
Pre-processing for single cell RNAseq: Hard thresholds, data (cluster)-driven or both?
scRNA-seq
updated 6 months ago by
yl759
▴ 120 • written 7 months ago by
psm
▴ 130
4
votes
3
replies
753
views
Creating custom GTF file for use with Cellranger with barcode sequences
Cellranger
7 months ago by
stefano.iantorno
▴ 70
4
votes
6
replies
955
views
Open-Source software. Good or bad for the market?
genomic-analysis
software
updated 11 months ago by
Ram
43k • written 6.2 years ago by
Bioinformatician90
• 0
4
votes
6
replies
804
views
how to plot SV(structural variants) from many assemblies of a given locus
SV
11 months ago by
natalev
▴ 20
4
votes
3
replies
1.0k
views
What is the difference between vst and rlog to perform PCA ?
rlog
PCA
vsd
updated 11 months ago by
ATpoint
82k • written 11 months ago by
Amr
▴ 160
4
votes
6
replies
2.6k
views
Convert Nanopore Fast5 files to Fasta format
fast5
fasta
Nanopore
11 months ago by
Sowmya Pulapet
▴ 70
4
votes
4
replies
480
views
Correlation for ATAC-Seq and Chip-Seq
RNA-Seq
Chip-Seq
ATAC-Seq
8 weeks ago by
qudrat.nii
▴ 10
4
votes
7
replies
2.4k
views
Batch effects vs biological variables
Batch-effect
DESeq2
combat_seq
updated 18 days ago by
Ram
43k • written 3.7 years ago by
l.uva
▴ 20
4
votes
4
replies
847
views
retaining only the clusters of interest
seurat
single-cell
scRna-seq
updated 10 months ago by
Ram
43k • written 10 months ago by
shamza
• 0
4
votes
5
replies
538
views
Which refseq_protein db to choose for zingiberaceae
local
blastp
blast
updated 8 months ago by
GenoMax
141k • written 8 months ago by
Nilo
• 0
4
votes
3
replies
484
views
Parsing columns with awk
awk
updated 5 months ago by
Ram
43k • written 5 months ago by
pablo
▴ 300
4
votes
2
replies
627
views
Visualization package for Maf Files using Python
Python
maftools
Visualization
MAF
updated 6 months ago by
Mark
★ 1.5k • written 6 months ago by
Manuel Sokolov Ravasqueira
▴ 100
4
votes
3
replies
312
views
Getting less DE genes when incorporating all samples
RNA-seq
differential-expression
deseq2
updated 10 weeks ago by
jv
★ 1.8k • written 10 weeks ago by
shome
▴ 10
4
votes
3
replies
392
views
Single cell analysis of Cancer
cancer
single-cell
RNA-seq
updated 10 weeks ago by
GenoMax
141k • written 10 weeks ago by
moustafa_abohawya
▴ 20
4
votes
11
replies
1.8k
views
PCA WITH PLINK
PLINK
updated 8 months ago by
Kevin Blighe
87k • written 8 months ago by
Michelle Guerra
• 0
4
votes
12
replies
7.8k
views
6 follow
BWA error: no ID within the read group line
bwa
readgroups
RG
parallel
updated 11 weeks ago by
mgdrnl
▴ 10 • written 3.4 years ago by
whb
▴ 60
4
votes
6
replies
339
views
Protein loops
protein
Loop
6 weeks ago by
Curious
▴ 10
4
votes
8
replies
1.2k
views
Error executing nf-core/metaboigniter pipeline
nf-core
metaboigniter
nextflow
updated 8 months ago by
Phil Ewels
★ 1.4k • written 8 months ago by
eesha28112001
• 0
4
votes
4
replies
3.3k
views
Unable to install Autogrid4
autogrid
software-error
autogrid4
updated 11 months ago by
Ram
43k • written 3.1 years ago by
roybatty269
• 0
4
votes
14
replies
1.1k
views
remove white space in fastq file
fastq
updated 4 months ago by
GenoMax
141k • written 4 months ago by
gkarere
• 0
4
votes
16
replies
957
views
hisat2 location does not exist
hisat2
updated 8 weeks ago by
Ram
43k • written 9 weeks ago by
Eric
• 0
4
votes
8
replies
1.9k
views
Hello, I have differential ATAC-seq from control and diseased cells (H3K27ac mark as chromatin mark) and wondering how to call enhancers using ROSE …
super-enhancers
Enhancers
updated 12 weeks ago by
jared.andrews07
★ 16k • written 3 months ago by
Manhezz
• 0
4
votes
5
replies
384
views
Filter out miRNA from ncRNA dataset
bowtie
bowtie2
miRNA
filtering
ncRNA
updated 9 weeks ago by
ATpoint
82k • written 9 weeks ago by
binaryCode
▴ 10
4
votes
9
replies
2.6k
views
Blast+ remote database names
blast
remote
databases
Blastplus
updated 9 months ago by
GenoMax
141k • written 2.3 years ago by
Komalharini
• 0
4
votes
5
replies
2.4k
views
Merge CNVnator output of multiple samples
CNV
WGS
updated 10 months ago by
Ram
43k • written 6.7 years ago by
zhang248
▴ 40
4
votes
4
replies
605
views
I cannot install anaconda on ubuntu 22.04
ubuntu
anaconda
Conda
updated 8 months ago by
Ram
43k • written 8 months ago by
Omar
▴ 10
4
votes
3
replies
727
views
Why is there a big difference between the outputs of `geneBody_coverage` of `RSeQC` when using different bed files?
RSeQC
11 months ago by
Dan
▴ 180
4
votes
6
replies
1.2k
views
Transcript quantification
rna-seq
transcriptome
SRA
updated 10 months ago by
ATpoint
82k • written 10 months ago by
firefox91
• 0
4
votes
7
replies
812
views
SNP IDs
SNP
5 months ago by
kl
▴ 10
4
votes
6
replies
633
views
Unexpected separation of RNA-seq samples on PCA plot
depletion
PCA
rRNA
plot
RNA-seq
5 months ago by
Tihana
▴ 10
4
votes
6
replies
934
views
How to pass from DNA to AA fasta
genetics
updated 11 months ago by
Buffo
★ 2.4k • written 11 months ago by
Anderson Stiward
• 0
4
votes
12
replies
3.5k
views
How to read VCF (v4.1) file? (student project) (samtools version 0.1.19)
variant-calling
samtools
VCF
BCF
updated 4 weeks ago by
Ram
43k • written 5.5 years ago by
c.clarido
▴ 110
4
votes
7
replies
565
views
Can any JBrowse2 tracks show multiple colors for reads at different nucleotide positions?
JBrowse
JBrowse2
updated 24 days ago by
cmdcolin
★ 3.8k • written 28 days ago by
I0110
▴ 140
4
votes
1
reply
563
views
How to Load a Molecular Signature Database into clusterProfiler gseGO?
ClusterProfiler
RNA-seq
GSEA
updated 9 months ago by
Nitin Narwade
★ 1.6k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
1,000 results • Page
3 of 20
Recent Votes
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
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Comment: Create a new bed file with all pairwise combinations between two other bed files
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Recent Awards •
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35k
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▴ 40
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141k
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Recent Replies
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
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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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