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412 results • Page
2 of 9
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Votes
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50
votes
1
reply
8.9k
views
Tutorial:
Basic normalization, batch correction and visualization of RNA-seq data
edger
RNA-seq
updated 15 months ago by
Ram
43k • written 3.7 years ago by
ATpoint
82k
50
votes
7
replies
11k
views
7 follow
Tutorial:
Genome Assembly Review Papers
assembly
papers
updated 15 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
50
votes
30
replies
11k
views
13 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
updated 7 weeks ago by
Istvan Albert
100k • written 8.2 years ago by
Ram
43k
47
votes
19
replies
14k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control
fastqc
updated 16 months ago by
Ram
43k • written 11.2 years ago by
Istvan Albert
100k
46
votes
13
replies
15k
views
13 follow
Tutorial:
Methylation Analysis Tutorial in R - Part 1
R
cancer
methylation
updated 9 weeks ago by
Konstantinos
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
46
votes
6
replies
25k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 2.3 years ago by
cameron.cowan
▴ 50 • written 3.1 years ago by
rpolicastro
13k
45
votes
3
replies
13k
views
Tutorial:
A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics
computational-biology
updated 13 months ago by
Ram
43k • written 8.1 years ago by
Sinji
★ 3.2k
45
votes
2
replies
37k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 15 months ago by
Ram
43k • written 12.1 years ago by
MSU course 2011
▴ 540
43
votes
6
replies
12k
views
Tutorial:
Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl
maf
tcga
vcf
updated 14 months ago by
Ram
43k • written 10.3 years ago by
Cyriac Kandoth
6.1k
42
votes
2
replies
18k
views
Tutorial:
Sequencing Technology Review Papers
sequencing
papers
updated 15 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
42
votes
19
replies
7.9k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 14 months ago by
Ram
43k • written 11.2 years ago by
Daniel Standage
4.1k
42
votes
16
replies
24k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 21 months ago by
Ram
43k • written 8.7 years ago by
Chirag Nepal
★ 2.4k
40
votes
9
replies
11k
views
10 follow
Tutorial:
Resources for flow cytometry bioinformatics
single-cell
flow-cytometry
updated 14 months ago by
Ram
43k • written 10.1 years ago by
Ahill
★ 1.9k
39
votes
16
replies
37k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 4 months ago by
GenoMax
142k • written 3.8 years ago by
lavinia.gordon
▴ 160
39
votes
6
replies
20k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 12 months ago by
Ram
43k • written 6.7 years ago by
steve
★ 3.5k
37
votes
5
replies
6.1k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 8 months ago by
gallardodiazmiriam
▴ 20 • written 8.8 years ago by
Luke Crichton
▴ 430
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 12 months ago by
GenoMax
142k • written 10.5 years ago by
Obi Griffith
20k
35
votes
13
replies
14k
views
9 follow
Tutorial:
How to get FASTQ reads from the Short Read Archive (SRA)
fastq
sra
updated 2.3 years ago by
liorglic
★ 1.4k • written 2.6 years ago by
Istvan Albert
100k
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 14 months ago by
Ram
43k • written 10.6 years ago by
Istvan Albert
100k
34
votes
15
replies
6.6k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 14 months ago by
Ram
43k • written 4.9 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 8 weeks ago by
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
32
votes
4
replies
8.0k
views
Tutorial:
Fast LD computation from VCF files using tomahawk
ld
snp
vcf
vcftools
bcftools
updated 14 months ago by
Ram
43k • written 5.5 years ago by
firestar
★ 1.6k
32
votes
6
replies
12k
views
Tutorial:
A simple tutorial for a complex ComplexHeatmap
clustering
pam
arthritis
ComplexHeatmap
updated 14 months ago by
Ram
43k • written 4.0 years ago by
Kevin Blighe
88k
31
votes
8
replies
11k
views
7 follow
Tutorial:
How To Create A Bioinformatics Pipeline Using Spotify !
python
pipeline
updated 14 months ago by
Ram
43k • written 10.1 years ago by
Rad
▴ 810
30
votes
14
replies
16k
views
8 follow
Tutorial:
Installation of the MuSiC suite on unsupported Linux distributions
genome-music
linux
smg
updated 14 months ago by
Ram
43k • written 11.3 years ago by
Cyriac Kandoth
6.1k
30
votes
6
replies
22k
views
Tutorial:
Transforming And Manipulating Color Space Reads
conversion
solid
updated 20 months ago by
Ram
43k • written 12.1 years ago by
Istvan Albert
100k
30
votes
10
replies
83k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 14 months ago by
Ram
43k • written 3.2 years ago by
Nitin Narwade
★ 1.6k
29
votes
5
replies
6.4k
views
Tutorial:
Gnu Parallel Tutorial
parallel
gnu-parallel
updated 14 months ago by
Ram
43k • written 10.7 years ago by
ole.tange
★ 4.4k
29
votes
4
replies
4.5k
views
Tutorial:
Modern Statistics for Modern Biology
statistics
updated 14 months ago by
Ram
43k • written 5.3 years ago by
Jean-Karim Heriche
27k
28
votes
0
replies
3.7k
views
Tutorial:
Building Docker images
singularity
docker
container
22 months ago by
ATpoint
82k
26
votes
0
replies
2.5k
views
Tutorial:
Resources / databases for clinical interpretation of cancer variants
interpretation
cancer
annotation
variant
updated 14 months ago by
Ram
43k • written 4.6 years ago by
Malachi Griffith
20k
26
votes
17
replies
7.8k
views
8 follow
Tutorial:
virtualenv - running Python based software in isolation
python
virtualenv
updated 20 months ago by
Ram
43k • written 9.8 years ago by
Ian
6.0k
26
votes
15
replies
8.9k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
course
training
mooc
updated 14 months ago by
Ram
43k • written 11.3 years ago by
Medhat
9.7k
24
votes
4
replies
7.7k
views
Tutorial:
Using EnrichedHeatmap for visualization of NGS experiments
heatmap
chip-seq
atac-seq
EnrichedHeatmap
updated 14 months ago by
Ram
43k • written 4.8 years ago by
ATpoint
82k
23
votes
19
replies
6.9k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
fastq
mutation
cancer
target
updated 13 months ago by
Ram
43k • written 7.6 years ago by
chen
★ 2.5k
23
votes
8
replies
5.4k
views
Tutorial:
A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K
methylation
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
brentp
24k
23
votes
2
replies
5.9k
views
Tutorial:
Extracting genomic feature sequences from GTF/GFF files with AGAT
extract
GTF
GFF
sequence
updated 20 months ago by
eggrandio
▴ 40 • written 3.1 years ago by
Juke34
8.6k
22
votes
1
reply
3.2k
views
Tutorial:
Introduction To R Course Materials Available
R
updated 16 months ago by
Ram
43k • written 12.1 years ago by
Sean Davis
26k
22
votes
10
replies
7.1k
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse
gene
R
updated 14 months ago by
Ram
43k • written 3.7 years ago by
rpolicastro
13k
22
votes
2
replies
6.0k
views
Tutorial:
Use a workflow management tool to manage your computational pipelines
workflow-management
snakemake
pipeline
updated 13 months ago by
Ram
43k • written 7.5 years ago by
Eric Lim
★ 2.1k
21
votes
5
replies
6.8k
views
Tutorial:
Analysis of single-cell RNA-seq data
single-cell
RNA-Seq
updated 13 months ago by
Ram
43k • written 7.9 years ago by
Geparada
★ 1.5k
21
votes
9
replies
6.6k
views
8 follow
Tutorial:
Interactive Perl Learning
perl
updated 14 months ago by
Ram
43k • written 10.9 years ago by
Medhat
9.7k
21
votes
26
replies
9.8k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 9 weeks ago by
Yao
▴ 30 • written 4.5 years ago by
Juke34
8.6k
21
votes
13
replies
11k
views
10 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 6 months ago by
jude
• 0 • written 22 months ago by
ATpoint
82k
20
votes
2
replies
8.1k
views
Tutorial:
Creating a karyotype plot with genes using karyoploteR
karyoploteR
visualization
R
genome
updated 12 months ago by
Ram
43k • written 6.5 years ago by
bernatgel
★ 3.4k
20
votes
2
replies
3.4k
views
Tutorial:
Beginner's Handbook to Next Generation Sequencing
NGS
updated 12 months ago by
Ram
43k • written 7.1 years ago by
support
▴ 650
20
votes
6
replies
5.7k
views
Tutorial:
Open Targets and programmatic access
open-targets
disease
API
drug
updated 14 months ago by
Ram
43k • written 7.7 years ago by
Denise CS
★ 5.2k
20
votes
0
replies
8.8k
views
Tutorial:
Metagenomics Review Papers
metagenomics
papers
updated 15 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
20
votes
4
replies
2.7k
views
Tutorial:
Bash One-liners collection on Github
bash
linux
shell
updated 14 months ago by
Ram
43k • written 5.0 years ago by
nim.1111.ou
▴ 180
20
votes
14
replies
4.1k
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 13 months ago by
Ram
43k • written 8.0 years ago by
Mads Lerdrup
▴ 460
412 results • Page
2 of 9
Recent Votes
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
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Answer: TFs and Gene databases
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Differentially Expressed Genes between two conditions (scRNA, single GEO dataset with multiple samples and no cell annotations)
Differentially expressed genes between Seurat objects
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Recent Replies
Comment: Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
[Here](https://www.biostars.org/p/9544689/) is a forum post that may answer your question.
Comment: zero TPM for many gene including housekeeping when using kallisto
by
ashkan
▴ 160
@atpoint I checked all transcripts of GAPDH. they all have 0 TPM.
Comment: how to treat the replicates while performing WGCNA
by
andres.firrincieli
3.6k
> 1) I do not want to merge the MEs rather I asked about replicates, as > some replicates of same sample are showing different behavior for…
Comment: How to systematically check if a bam file is truncated
by
alanh
▴ 170
For more details about what `samtools quickcheck` actually checks for, add a few `-v`'s to the command line. $ samtools quickcheck -…
Comment: How to handle duplicated genes in TCGA data?
by
Zhenyu Zhang
★ 1.2k
Second what is said above, ensembl_id is the unique identifier. As a good bioinformatics habit, always use unique identifier for your anal…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
It doesn't work. The annotation labels are still in a default fontsize. I cant find a way to set the fontsize.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Yes. The solution to most things with ComplexHeatmap is to play around with parameters.
Comment: Reconstruction of locus, order contigs
by
BATMAN
• 0
I do not want to re-annotate the genome. I ask if there is a way to extract the region aligned with the mauve, in .gbk format.
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thank you. What exactly do you mean? Changing `ha = rowAnnotation(text = anno_mark(at = mark_at, labels = gene_names_interesting_in_cluster…
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
Ram
43k
Try tweaking the `gp` of the rowAnnotation instead of tweaking the `annotation_name_gp` - that might do the trick.
Comment: Help! Reconstruction of locus, order contigs
by
dthorbur
★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Details on salmon index
by
Rob
6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
Comment: Help! Reconstruction of locus, order contigs
by
BATMAN
• 0
Thanks for your reply, my idea is not to have to write it down. What I have is an alignment of the .gbk from the progressiveMauve. It would…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
I did some digging aroumd, no static binary. Plus it seems you need to roll your own program.
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
by
Gabriel R.
★ 2.9k
We tested it, however, it does not seem to produce a fast a file of the results or anything that we can easily parse. It produces a CIGAR a…
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