Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : all time
all time
today
this week
this month
this year
408 results • Page
2 of 9
Sort: Votes
Rank
Views
Votes
Replies
50
votes
3
replies
4.7k
views
Tutorial:
[[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 12 months ago by
Ram
43k • written 5.2 years ago by
ATpoint
81k
49
votes
1
reply
8.6k
views
Tutorial:
Basic normalization, batch correction and visualization of RNA-seq data
edger
RNA-seq
updated 13 months ago by
Ram
43k • written 3.5 years ago by
ATpoint
81k
49
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 19 minutes ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
47
votes
19
replies
13k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control
fastqc
updated 14 months ago by
Ram
43k • written 11.1 years ago by
Istvan Albert
100k
46
votes
13
replies
14k
views
13 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 16 days ago by
Konstantinos
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
45
votes
2
replies
37k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 13 months ago by
Ram
43k • written 12.0 years ago by
MSU course 2011
▴ 540
44
votes
6
replies
24k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 2.2 years ago by
cameron.cowan
▴ 40 • written 3.0 years ago by
rpolicastro
13k
44
votes
3
replies
13k
views
Tutorial:
A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics
computational-biology
updated 11 months ago by
Ram
43k • written 8.0 years ago by
Sinji
★ 3.2k
43
votes
6
replies
12k
views
Tutorial:
Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl
maf
tcga
vcf
updated 13 months ago by
Ram
43k • written 10.2 years ago by
Cyriac Kandoth
6.0k
42
votes
19
replies
7.8k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 13 months ago by
Ram
43k • written 11.1 years ago by
Daniel Standage
4.1k
42
votes
16
replies
23k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 19 months ago by
Ram
43k • written 8.5 years ago by
Chirag Nepal
★ 2.4k
42
votes
2
replies
18k
views
Tutorial:
Sequencing Technology Review Papers
sequencing
papers
updated 13 months ago by
Ram
43k • written 11.6 years ago by
Istvan Albert
100k
40
votes
9
replies
11k
views
10 follow
Tutorial:
Resources for flow cytometry bioinformatics
single-cell
flow-cytometry
updated 12 months ago by
Ram
43k • written 10.0 years ago by
Ahill
★ 1.9k
39
votes
6
replies
19k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 10 months ago by
Ram
43k • written 6.6 years ago by
steve
★ 3.5k
39
votes
16
replies
35k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 3 months ago by
GenoMax
140k • written 3.6 years ago by
lavinia.gordon
▴ 160
36
votes
5
replies
6.0k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 6 months ago by
gallardodiazmiriam
▴ 20 • written 8.7 years ago by
Luke Crichton
▴ 410
35
votes
17
replies
16k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning
classification
updated 10 months ago by
GenoMax
140k • written 10.4 years ago by
Obi Griffith
20k
34
votes
15
replies
6.4k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 12 months ago by
Ram
43k • written 4.8 years ago by
Shicheng Guo
★ 9.4k
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 9 days ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
34
votes
12
replies
30k
views
7 follow
Tutorial:
So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control
fastqc
updated 13 months ago by
Ram
43k • written 10.4 years ago by
Istvan Albert
100k
33
votes
13
replies
14k
views
9 follow
Tutorial:
How to get FASTQ reads from the Short Read Archive (SRA)
fastq
sra
updated 2.2 years ago by
liorglic
★ 1.3k • written 2.5 years ago by
Istvan Albert
100k
32
votes
6
replies
12k
views
Tutorial:
A simple tutorial for a complex ComplexHeatmap
clustering
pam
arthritis
ComplexHeatmap
updated 12 months ago by
Ram
43k • written 3.9 years ago by
Kevin Blighe
87k
32
votes
4
replies
7.8k
views
Tutorial:
Fast LD computation from VCF files using tomahawk
ld
snp
vcf
vcftools
bcftools
updated 12 months ago by
Ram
43k • written 5.4 years ago by
firestar
★ 1.6k
31
votes
8
replies
11k
views
7 follow
Tutorial:
How To Create A Bioinformatics Pipeline Using Spotify !
python
pipeline
updated 12 months ago by
Ram
43k • written 10.0 years ago by
Rad
▴ 810
30
votes
6
replies
22k
views
Tutorial:
Transforming And Manipulating Color Space Reads
conversion
solid
updated 18 months ago by
Ram
43k • written 11.9 years ago by
Istvan Albert
100k
30
votes
14
replies
16k
views
8 follow
Tutorial:
Installation of the MuSiC suite on unsupported Linux distributions
genome-music
linux
smg
updated 13 months ago by
Ram
43k • written 11.1 years ago by
Cyriac Kandoth
6.0k
29
votes
5
replies
6.3k
views
Tutorial:
Gnu Parallel Tutorial
parallel
gnu-parallel
updated 13 months ago by
Ram
43k • written 10.5 years ago by
ole.tange
★ 4.4k
29
votes
10
replies
80k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 12 months ago by
Ram
43k • written 3.0 years ago by
Nitin Narwade
★ 1.6k
28
votes
4
replies
4.4k
views
Tutorial:
Modern Statistics for Modern Biology
statistics
updated 12 months ago by
Ram
43k • written 5.2 years ago by
Jean-Karim Heriche
27k
28
votes
0
replies
3.6k
views
Tutorial:
Building Docker images
singularity
docker
container
20 months ago by
ATpoint
81k
26
votes
0
replies
2.4k
views
Tutorial:
Resources / databases for clinical interpretation of cancer variants
interpretation
cancer
annotation
variant
updated 12 months ago by
Ram
43k • written 4.5 years ago by
Malachi Griffith
19k
26
votes
17
replies
7.7k
views
8 follow
Tutorial:
virtualenv - running Python based software in isolation
python
virtualenv
updated 18 months ago by
Ram
43k • written 9.6 years ago by
Ian
6.0k
25
votes
15
replies
8.8k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
course
training
mooc
updated 13 months ago by
Ram
43k • written 11.2 years ago by
Medhat
9.7k
24
votes
4
replies
7.5k
views
Tutorial:
Using EnrichedHeatmap for visualization of NGS experiments
heatmap
chip-seq
atac-seq
EnrichedHeatmap
updated 12 months ago by
Ram
43k • written 4.6 years ago by
ATpoint
81k
23
votes
19
replies
6.8k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
fastq
mutation
cancer
target
updated 11 months ago by
Ram
43k • written 7.5 years ago by
chen
★ 2.5k
23
votes
8
replies
5.3k
views
Tutorial:
A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K
methylation
updated 2.3 years ago by
Ram
43k • written 9.6 years ago by
brentp
24k
22
votes
2
replies
6.0k
views
Tutorial:
Use a workflow management tool to manage your computational pipelines
workflow-management
snakemake
pipeline
updated 11 months ago by
Ram
43k • written 7.4 years ago by
Eric Lim
★ 2.1k
22
votes
10
replies
6.9k
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse
gene
R
updated 12 months ago by
Ram
43k • written 3.6 years ago by
rpolicastro
13k
22
votes
2
replies
5.6k
views
Tutorial:
Extracting genomic feature sequences from GTF/GFF files with AGAT
extract
GTF
GFF
sequence
updated 18 months ago by
eggrandio
▴ 40 • written 2.9 years ago by
Juke34
8.5k
22
votes
1
reply
3.2k
views
Tutorial:
Introduction To R Course Materials Available
R
updated 14 months ago by
Ram
43k • written 11.9 years ago by
Sean Davis
26k
21
votes
5
replies
6.7k
views
Tutorial:
Analysis of single-cell RNA-seq data
single-cell
RNA-Seq
updated 11 months ago by
Ram
43k • written 7.8 years ago by
Geparada
★ 1.5k
21
votes
26
replies
9.4k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 13 days ago by
Yao
▴ 30 • written 4.3 years ago by
Juke34
8.5k
21
votes
9
replies
6.5k
views
8 follow
Tutorial:
Interactive Perl Learning
perl
updated 13 months ago by
Ram
43k • written 10.8 years ago by
Medhat
9.7k
20
votes
2
replies
8.0k
views
Tutorial:
Creating a karyotype plot with genes using karyoploteR
karyoploteR
visualization
R
genome
updated 10 months ago by
Ram
43k • written 6.3 years ago by
bernatgel
★ 3.4k
20
votes
4
replies
8.6k
views
Tutorial:
DE analysis by edgeR
RNA-Seq
R
edgeR
updated 11 months ago by
Ram
43k • written 7.5 years ago by
zizigolu
★ 4.3k
20
votes
4
replies
2.6k
views
Tutorial:
Bash One-liners collection on Github
bash
linux
shell
updated 12 months ago by
Ram
43k • written 4.9 years ago by
nim.1111.ou
▴ 180
20
votes
14
replies
3.9k
views
Tutorial:
Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq
visualization
Windows
EaSeq
updated 11 months ago by
Ram
43k • written 7.9 years ago by
Mads Lerdrup
▴ 460
20
votes
0
replies
8.7k
views
Tutorial:
Metagenomics Review Papers
metagenomics
papers
updated 13 months ago by
Ram
43k • written 11.6 years ago by
Istvan Albert
100k
20
votes
7
replies
6.3k
views
Tutorial:
Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2
RNA-Seq
R
updated 12 months ago by
Ram
43k • written 5.5 years ago by
ahmad mousavi
▴ 800
20
votes
4
replies
14k
views
Tutorial:
How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor
affymetrix
updated 13 months ago by
Ram
43k • written 11.0 years ago by
Obi Griffith
20k
408 results • Page
2 of 9
Recent Votes
Comment: struggle to get fasta files from ucsc goldenPath
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
Quantile normalizing prior to or after TPM scaling?
Structural variant filtering
Trouble with bedtools getfasta
Gnu Parallel - Parallelize Serial Command Line Programs Without Changing Them
Answer: Hybrid assembly Pacbio- Nanopore
Recent Locations •
All
Hyderabad,
just now
Osaka,
3 minutes ago
Finland,
3 minutes ago
UK,
4 minutes ago
United States,
4 minutes ago
United Kingdom,
4 minutes ago
United Kingdom,
7 minutes ago
Recent Awards •
All
Scholar
to
Pierre Lindenbaum
160k
Popular Question
to
beacamara
• 0
Scholar
to
Devon Ryan
104k
Popular Question
to
blur
▴ 280
Popular Question
to
ATpoint
81k
Teacher
to
Haci
▴ 550
Popular Question
to
chevivien
▴ 90
Recent Replies
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Can you select the output format as sequence instead of BED?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Could you please elaborate how to retrieve the sequences directly from the table browser? Thanks!
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If coordinates in your BED file refer to chromosomal locations then you need to use the whole genome file and get those sections by the met…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
Istvan Albert
100k
maybe it would work better to ask the OP to post their question as a new one and delete this answer after, if you delete the post they ca…
Comment: Issue with making local BLAST database
by
GenoMax
140k
By default only 20 entries are returned if you don't set the `retmax` parameter. You will not want to do this via R since you will be limit…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
So this is my approach: I want to interrogate gene PVT1, I know the coordinates for it is chr8:127794532-128101252 In UCSC table I selected…
Comment: Flow Cytometry Data Analysis by Seurat
by
ATpoint
81k
> I think Seurat is suitable for our purpose (e.g. conducting dimensional reduction of the data such as tSNE), but does it make sense? No…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
mRNA file is not going to have the same co-ordinates as the main chromosomes. Can you clarify what coordinates are in your BED file?
Comment: Downloading a list of all refseq assembly ids, including supressed assembliey
by
GenoMax
140k
Can you provide examples of suppressed ID's?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
It is because I want to pull the mRNA fasta files and not DNA (which I guess is the case if I pull it from the entire genome)
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If your intervals are for main chromosomes why are you using the mRNA file instead of the entire genome? If you have the gene ID's you coul…
Answer: diffbind : killed dba.count(DBsample, bParallel=FALSE)
by
Pierre Lindenbaum
160k
I downsampled the bams and it works now...
Answer: ONT direct RNA sequencing
by
dthorbur
★ 1.7k
You can check the validity of gzipped files using `gzip -v -t file.gz`. Should look something like this: ``` $ gzip -v -t test_file.…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
I tested seqtk sample but I generate a wird result. Can I share my code and results with you please ?
Comment: Nextflow ERROR : Timeout waiting for connection from pool
by
GenoMax
140k
As best as I can tell it is a combination of things. Did you try setting `export NXF_ENABLE_VIRTUAL_THREADS="true"` in your shell? You also…
Traffic: 2522 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6