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408 results • Page
2 of 9
Sort: Votes
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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 14 hours 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 17 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
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
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
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
16
replies
36k
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
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
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
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 10.5 years ago by
Istvan Albert
100k
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
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
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 11.2 years ago by
Cyriac Kandoth
6.0k
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
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
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
28
votes
0
replies
3.6k
views
Tutorial:
Building Docker images
singularity
docker
container
20 months ago by
ATpoint
81k
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
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
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
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
1
reply
3.2k
views
Tutorial:
Introduction To R Course Materials Available
R
updated 15 months ago by
Ram
43k • written 11.9 years ago by
Sean Davis
26k
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
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
21
votes
26
replies
9.4k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 14 days ago by
Yao
▴ 30 • written 4.3 years ago by
Juke34
8.5k
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
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
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
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
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
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
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 6.4 years ago by
bernatgel
★ 3.4k
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
6
replies
5.5k
views
Tutorial:
Open Targets and programmatic access
open-targets
disease
API
drug
updated 12 months ago by
Ram
43k • written 7.5 years ago by
Denise CS
★ 5.2k
408 results • Page
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Recent Votes
Answer: log2(TPM+1)
Comment: Error in openning FastQC
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
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Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Yikes. Well, this is from an Illumina MiniSeq. Sure, I will use alignment, but only to remove host reads. Then the remaining reads will go …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
This is going to be tough to diagnose. Are you going to align to a reference? If so go ahead with the alignments to see if alignments turn …
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
BRENO
• 0
Thank you for replying. I have separated the reads with at least one N on them and they account for 0.2% of the total reads in the file (8'…
Comment: Error running local blastn in R using system2
by
Mensur Dlakic
★ 26k
The `-db data/nt_euk` switch means that in your current directory you have a subdirectory called `data`, and all the `nt_euk` files are in …
Comment: Low number of both surviving reads after trimming
by
Jay
• 0
Thank you for your opinion. I will try with lower LEADING and TRAILING bases. By the way, I tried to set `keepBothReads:true` through sear…
Comment: Error in openning FastQC
by
GenoMax
140k
At this point it would be beneficial to learn some of the basics of command line. Please use this UNIX tutorial since you seem to be new to…
Comment: vcf file: number of samples does not match number of columns
by
Pierre Lindenbaum
160k
> ore or have any suggestions for fixing it? it's a problem with your upstream process. You'd better fix it.
Comment: Error in openning FastQC
by
friszd
• 0
after running fastqc -o output.html input.fastq, terminal returns: " Specified output directory 'output.html' does not exist " , when i run…
Comment: Is it reasonable to discard reads that show variation of quality across its leng
by
GenoMax
140k
The question you should be looking into is why the Q scores are dropping there? Are there `N` calls indicating some issue with that cycle?
Comment: Error in openning FastQC
by
GenoMax
140k
What is `ctrl+c ctrl+v`? You may actually be killing the running fastqc process. If you run `fastqc` interactively (like what was shown ab…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Dave Carlson
★ 1.7k
Ugh. I've definitely done this one before as well. And was none too happy about it.
Comment: Error in openning FastQC
by
friszd
• 0
fastqc -o output.html input.fastq ctrl+c ctrl+v
Comment: Error running local blastn in R using system2
by
GenoMax
140k
What do you see if you `cat nt_euk.nal`? Do the number of pieces mentioned in that file match with what you locally have?
Comment: Low number of both surviving reads after trimming
by
GenoMax
140k
It is your data and if you want to do that it is up to you. You may be throwing away essentially good data (you should remove the nextera s…
Comment: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Istvan Albert
100k
Some things never change ... the most common mistake is still the one on top there
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