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379 results • Page
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50
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1
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7.4k
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Tutorial:
Basic normalization, batch correction and visualization of RNA-seq data
edger
RNA-seq
updated 7 months ago by
Ram
40k • written 3.1 years ago by
ATpoint
77k
49
votes
7
replies
11k
views
7 follow
Tutorial:
Genome Assembly Review Papers
assembly
papers
updated 7 months ago by
Ram
40k • written 11.1 years ago by
Istvan Albert
98k
48
votes
28
replies
8.6k
views
9 follow
Tutorial:
How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation
meta
how-to
4 months ago by
Ram
40k
47
votes
19
replies
13k
views
8 follow
Tutorial:
Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control
fastqc
updated 8 months ago by
Ram
40k • written 10.6 years ago by
Istvan Albert
98k
45
votes
2
replies
36k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 7 months ago by
Ram
40k • written 11.5 years ago by
MSU course 2011
▴ 540
44
votes
3
replies
12k
views
Tutorial:
A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics
computational-biology
updated 6 months ago by
Ram
40k • written 7.5 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 7 months ago by
Ram
40k • written 9.7 years ago by
Cyriac Kandoth
6.0k
43
votes
6
replies
22k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 20 months ago by
cameron.cowan
▴ 40 • written 2.5 years ago by
rpolicastro
12k
42
votes
19
replies
7.4k
views
8 follow
Tutorial:
Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 7 months ago by
Ram
40k • written 10.6 years ago by
Daniel Standage
4.1k
42
votes
2
replies
17k
views
Tutorial:
Sequencing Technology Review Papers
sequencing
papers
updated 7 months ago by
Ram
40k • written 11.1 years ago by
Istvan Albert
98k
42
votes
16
replies
22k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 14 months ago by
Ram
40k • written 8.0 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 7 months ago by
Ram
40k • written 9.5 years ago by
Ahill
★ 1.9k
39
votes
6
replies
18k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 4 months ago by
Ram
40k • written 6.1 years ago by
steve
★ 3.3k
39
votes
8
replies
12k
views
10 follow
Tutorial:
Methylation Analysis Tutorial in R_part1
cancer
R
methylation
updated 6 months ago by
Ram
40k • written 3.0 years ago by
Hamid Ghaedi
3.0k
36
votes
5
replies
5.8k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 26 days ago by
gallardodiazmiriam
▴ 20 • written 8.2 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 5 months ago by
GenoMax
135k • written 9.9 years ago by
Obi Griffith
20k
34
votes
15
replies
19k
views
12 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 6 months ago by
Ram
40k • written 7.0 years ago by
martinguerrerog89
▴ 310
34
votes
15
replies
5.8k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 6 months ago by
Ram
40k • written 4.3 years ago by
Shicheng Guo
★ 9.3k
33
votes
9
replies
30k
views
11 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 6 months ago by
Ram
40k • written 3.1 years ago by
lavinia.gordon
▴ 160
32
votes
4
replies
7.1k
views
Tutorial:
Fast LD computation from VCF files using tomahawk
ld
snp
vcf
vcftools
bcftools
updated 6 months ago by
Ram
40k • written 4.9 years ago by
firestar
★ 1.6k
31
votes
8
replies
10k
views
7 follow
Tutorial:
How To Create A Bioinformatics Pipeline Using Spotify !
python
pipeline
updated 7 months ago by
Ram
40k • written 9.5 years ago by
Rad
▴ 810
31
votes
12
replies
28k
views
7 follow
Tutorial:
So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control
fastqc
updated 7 months ago by
Ram
40k • written 10.0 years ago by
Istvan Albert
98k
31
votes
6
replies
11k
views
Tutorial:
A simple tutorial for a complex ComplexHeatmap
clustering
pam
arthritis
ComplexHeatmap
updated 6 months ago by
Ram
40k • written 3.4 years ago by
Kevin Blighe
86k
30
votes
6
replies
21k
views
Tutorial:
Transforming And Manipulating Color Space Reads
conversion
solid
updated 12 months ago by
Ram
40k • written 11.4 years ago by
Istvan Albert
98k
30
votes
14
replies
16k
views
8 follow
Tutorial:
Installation of the MuSiC suite on unsupported Linux distributions
genome-music
linux
smg
updated 7 months ago by
Ram
40k • written 10.7 years ago by
Cyriac Kandoth
6.0k
29
votes
5
replies
6.1k
views
Tutorial:
Gnu Parallel Tutorial
parallel
gnu-parallel
updated 7 months ago by
Ram
40k • written 10.1 years ago by
ole.tange
★ 4.3k
28
votes
4
replies
4.1k
views
Tutorial:
Modern Statistics for Modern Biology
statistics
updated 6 months ago by
Ram
40k • written 4.7 years ago by
Jean-Karim Heriche
26k
28
votes
13
replies
11k
views
9 follow
Tutorial:
How to get FASTQ reads from the Short Read Archive (SRA)
fastq
sra
updated 20 months ago by
liorglic
★ 1.3k • written 23 months ago by
Istvan Albert
98k
27
votes
10
replies
70k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 6 months ago by
Ram
40k • written 2.5 years ago by
Nitin Narwade
★ 1.4k
27
votes
0
replies
3.3k
views
Tutorial:
Building Docker images
singularity
docker
container
14 months ago by
ATpoint
77k
26
votes
17
replies
7.2k
views
8 follow
Tutorial:
virtualenv - running Python based software in isolation
python
virtualenv
updated 12 months ago by
Ram
40k • written 9.1 years ago by
Ian
6.0k
26
votes
0
replies
2.3k
views
Tutorial:
Resources / databases for clinical interpretation of cancer variants
interpretation
cancer
annotation
variant
updated 6 months ago by
Ram
40k • written 4.0 years ago by
Malachi Griffith
19k
25
votes
15
replies
8.4k
views
8 follow
Tutorial:
Syllabus To Learn Bioinformatics From Online Video Resources
course
training
mooc
updated 7 months ago by
Ram
40k • written 10.7 years ago by
Medhat
9.7k
24
votes
4
replies
6.9k
views
Tutorial:
Using EnrichedHeatmap for visualization of NGS experiments
heatmap
chip-seq
atac-seq
EnrichedHeatmap
updated 6 months ago by
Ram
40k • written 4.1 years ago by
ATpoint
77k
23
votes
19
replies
6.2k
views
10 follow
Tutorial:
MutScan: Detect important mutations by scanning FastQ files directly
fastq
mutation
cancer
target
updated 5 months ago by
Ram
40k • written 7.0 years ago by
chen
★ 2.4k
23
votes
8
replies
5.1k
views
Tutorial:
A Practical (And Opinionated) Guide To Analyzing Human Methylation 450K Data
450K
methylation
updated 21 months ago by
Ram
40k • written 9.1 years ago by
brentp
24k
22
votes
1
reply
3.1k
views
Tutorial:
Introduction To R Course Materials Available
R
updated 9 months ago by
Ram
40k • written 11.5 years ago by
Sean Davis
26k
22
votes
2
replies
5.8k
views
Tutorial:
Use a workflow management tool to manage your computational pipelines
workflow-management
snakemake
pipeline
updated 5 months ago by
Ram
40k • written 6.9 years ago by
Eric Lim
★ 2.1k
21
votes
9
replies
6.3k
views
8 follow
Tutorial:
Interactive Perl Learning
perl
updated 7 months ago by
Ram
40k • written 10.3 years ago by
Medhat
9.7k
21
votes
10
replies
6.0k
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse
gene
R
updated 6 months ago by
Ram
40k • written 3.1 years ago by
rpolicastro
12k
21
votes
2
replies
4.8k
views
Tutorial:
Extracting genomic feature sequences from GTF/GFF files with AGAT
extract
GTF
GFF
sequence
updated 13 months ago by
eggrandio
▴ 40 • written 2.5 years ago by
Juke34
8.3k
20
votes
4
replies
2.4k
views
Tutorial:
Bash One-liners collection on Github
bash
linux
shell
updated 6 months ago by
Ram
40k • written 4.4 years ago by
nim.1111.ou
▴ 180
20
votes
2
replies
7.6k
views
Tutorial:
Creating a karyotype plot with genes using karyoploteR
karyoploteR
visualization
R
genome
updated 4 months ago by
Ram
40k • written 5.9 years ago by
bernatgel
★ 3.4k
20
votes
0
replies
8.5k
views
Tutorial:
Metagenomics Review Papers
metagenomics
papers
updated 7 months ago by
Ram
40k • written 11.1 years ago by
Istvan Albert
98k
20
votes
4
replies
14k
views
Tutorial:
How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor
affymetrix
updated 7 months ago by
Ram
40k • written 10.5 years ago by
Obi Griffith
20k
20
votes
7
replies
6.0k
views
Tutorial:
Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2
RNA-Seq
R
updated 6 months ago by
Ram
40k • written 5.0 years ago by
ahmad mousavi
▴ 760
20
votes
6
replies
5.2k
views
Tutorial:
Open Targets and programmatic access
open-targets
disease
API
drug
updated 6 months ago by
Ram
40k • written 7.0 years ago by
Denise CS
★ 5.2k
20
votes
5
replies
6.5k
views
Tutorial:
Analysis of single-cell RNA-seq data
single-cell
RNA-Seq
updated 6 months ago by
Ram
40k • written 7.3 years ago by
Geparada
★ 1.5k
20
votes
4
replies
8.4k
views
Tutorial:
DE analysis by edgeR
RNA-Seq
R
edgeR
updated 5 months ago by
Ram
40k • written 7.1 years ago by
fi1d18
★ 4.2k
20
votes
14
replies
3.6k
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 6 months ago by
Ram
40k • written 7.4 years ago by
Mads Lerdrup
▴ 460
379 results • Page
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Answer: 18S taxonomy assignment SILVA database formatting
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Comment: Error in checkFullRank(modelMatrix) :
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Basti
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Apart from the response below, your design is strange. Why did you want to adjust for sample if you want to compare the expression between …
Comment: 18S taxonomy assignment SILVA database formatting
by
mbuenner
• 0
Changing it a bit to $ awk 'BEGIN{FS=";"; OFS=";"} /^>/ { print $4,$5,$6,$7,$8;$9;$10; next; }; { print; }' SILVA_132_taxonomy_assignment…
Answer: 18S taxonomy assignment SILVA database formatting
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I'm not an expert on `awk`, but I tried the following and it seems to work. Instead of using the original downloaded file, give your latest…
Comment: 18S taxonomy assignment SILVA database formatting
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Thank you for editing the post and for your answer. Sadly, the linked formatted database does not contain Fungi, e.g. when I grep 'Fungi'…
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Thank you for your comment, but it did not help!
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Please, whenever you need to add more information, just edit your original post and do not add answers below unless you found the solution …
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Hi, I know this is an old thread, but I am encountering a similar problem. I am trying to do an msa for the cds sequences of 5 bumblebee sp…
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Hi! Please share first with us an example how the data looks like, the command-line you're running and the problem that you're getting. If…
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I may have stumbled on a solution for this problem. What I wanted was the SNPs or mutations in the VCF to be incorporated in the reference.…
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Thank you. I tried doing a pseudobulk analysis by doing the following: I have 9 patient ids in a column `Patient` in my metadata, and a co…
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How much memory does you machine have?
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It's recommended to make a `Tool` post with usage examples that you can link to.
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Software carpentry provides some good [introductory courses in Linux, Git, Python and R][1]. We are using these materials in our local soft…
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