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411 results • Page
2 of 9
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Votes
Replies
50
votes
3
replies
4.8k
views
Tutorial:
[[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 13 months ago by
Ram
43k • written 5.3 years ago by
ATpoint
82k
50
votes
1
reply
8.7k
views
Tutorial:
Basic normalization, batch correction and visualization of RNA-seq data
edger
RNA-seq
updated 14 months ago by
Ram
43k • written 3.6 years ago by
ATpoint
82k
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 4 weeks ago by
Istvan Albert
100k • written 8.2 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 15 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 7 weeks ago by
Konstantinos
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
45
votes
2
replies
37k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 14 months ago by
Ram
43k • written 12.1 years ago by
MSU course 2011
▴ 540
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
44
votes
6
replies
24k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 2.3 years ago by
cameron.cowan
▴ 40 • written 3.1 years ago by
rpolicastro
13k
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
6.0k
42
votes
2
replies
18k
views
Tutorial:
Sequencing Technology Review Papers
sequencing
papers
updated 14 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
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 21 months ago by
Ram
43k • written 8.6 years ago by
Chirag Nepal
★ 2.4k
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
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 10.0 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 4 months ago by
GenoMax
141k • written 3.7 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 11 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 7 months ago by
gallardodiazmiriam
▴ 20 • written 8.8 years ago by
Luke Crichton
▴ 430
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 2.5 years ago by
Istvan Albert
100k
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
141k • 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 6 weeks ago by
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
34
votes
15
replies
6.5k
views
6 follow
Tutorial:
How to do data cleaning for VCF genetic file
vcf
updated 13 months ago by
Ram
43k • written 4.9 years ago by
Shicheng Guo
★ 9.4k
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 10.5 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 13 months ago by
Ram
43k • written 3.9 years ago by
Kevin Blighe
87k
32
votes
4
replies
7.9k
views
Tutorial:
Fast LD computation from VCF files using tomahawk
ld
snp
vcf
vcftools
bcftools
updated 13 months ago by
Ram
43k • written 5.5 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 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 11.2 years ago by
Cyriac Kandoth
6.0k
30
votes
10
replies
81k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 13 months ago by
Ram
43k • written 3.1 years ago by
Nitin Narwade
★ 1.6k
30
votes
6
replies
22k
views
Tutorial:
Transforming And Manipulating Color Space Reads
conversion
solid
updated 19 months ago by
Ram
43k • written 12.0 years ago by
Istvan Albert
100k
29
votes
5
replies
6.4k
views
Tutorial:
Gnu Parallel Tutorial
parallel
gnu-parallel
updated 14 months ago by
Ram
43k • written 10.6 years ago by
ole.tange
★ 4.4k
29
votes
4
replies
4.5k
views
Tutorial:
Modern Statistics for Modern Biology
statistics
updated 13 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
21 months ago by
ATpoint
82k
26
votes
0
replies
2.4k
views
Tutorial:
Resources / databases for clinical interpretation of cancer variants
interpretation
cancer
annotation
variant
updated 13 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 19 months ago by
Ram
43k • written 9.7 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 13 months ago by
Ram
43k • written 4.7 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 12 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
22
votes
1
reply
3.2k
views
Tutorial:
Introduction To R Course Materials Available
R
updated 16 months ago by
Ram
43k • written 12.0 years ago by
Sean Davis
26k
22
votes
10
replies
7.0k
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse
gene
R
updated 13 months ago by
Ram
43k • written 3.7 years ago by
rpolicastro
13k
22
votes
2
replies
5.8k
views
Tutorial:
Extracting genomic feature sequences from GTF/GFF files with AGAT
extract
GTF
GFF
sequence
updated 19 months ago by
eggrandio
▴ 40 • written 3.0 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 12 months ago by
Ram
43k • written 7.5 years ago by
Eric Lim
★ 2.1k
21
votes
13
replies
10k
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
21
votes
9
replies
6.5k
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
5
replies
6.8k
views
Tutorial:
Analysis of single-cell RNA-seq data
single-cell
RNA-Seq
updated 12 months ago by
Ram
43k • written 7.8 years ago by
Geparada
★ 1.5k
21
votes
26
replies
9.6k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 6 weeks ago by
Yao
▴ 30 • written 4.4 years ago by
Juke34
8.5k
20
votes
4
replies
14k
views
Tutorial:
How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor
affymetrix
updated 14 months ago by
Ram
43k • written 11.1 years ago by
Obi Griffith
20k
20
votes
4
replies
2.6k
views
Tutorial:
Bash One-liners collection on Github
bash
linux
shell
updated 13 months ago by
Ram
43k • written 5.0 years ago by
nim.1111.ou
▴ 180
20
votes
2
replies
8.1k
views
Tutorial:
Creating a karyotype plot with genes using karyoploteR
karyoploteR
visualization
R
genome
updated 11 months ago by
Ram
43k • written 6.4 years ago by
bernatgel
★ 3.4k
20
votes
2
replies
3.4k
views
Tutorial:
Beginner's Handbook to Next Generation Sequencing
NGS
updated 11 months ago by
Ram
43k • written 7.1 years ago by
support
▴ 650
20
votes
4
replies
8.6k
views
Tutorial:
DE analysis by edgeR
RNA-Seq
R
edgeR
updated 12 months ago by
Ram
43k • written 7.6 years ago by
zizigolu
★ 4.3k
20
votes
7
replies
6.4k
views
Tutorial:
Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2
RNA-Seq
R
updated 13 months ago by
Ram
43k • written 5.5 years ago by
ahmad mousavi
▴ 800
411 results • Page
2 of 9
Recent Votes
Programmatically retrieving positions of protein active site residues
Programmatically retrieving positions of protein active site residues
A: Can Biopython Properly Import Fasta Headers With Spaces In Them?
Programmatically retrieving positions of protein active site residues
Answer: Polishing genome assembly
Answer: Integrate transcriptomic data and proteomics data.
Answer: Integrate transcriptomic data and proteomics data.
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Comment: Adjust pvalue in R with different approach give me all different outcome
by
Aspire
▴ 300
- p.adjust() is supposed to receive a **numeric vector of p-values**, not a matrix. - It makes no sense to "adjust" just one p-value, as…
Comment: Downsampling fastq file
by
marco.barr
▴ 80
I understood where the problem lies. I discussed with my wet lab colleagues (this is part of a bioinformatician's job...) and by showing th…
Comment: Programmatically retrieving positions of protein active site residues
by
me
▴ 760
This question fits in nicely with the [SIB Swiss Institute of Bioinformatics course on Enzyme information in UniProt][1] [1]: https://w…
Answer: Programmatically retrieving positions of protein active site residues
by
me
▴ 760
This can be done via SPARQL at the UniProt.org sparql endpoint PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX fald…
Comment: KEGG Pathways
by
Sudip
• 0
No it does not. Do you know of a way that can help me achieve what I want?
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
by
GenoMax
141k
UniRef file is 43G compressed so probably will become ~60G when uncompressed. You would likely be looking at at least that much +10-20% GB …
Comment: RNAseq one control two conditions, shared and exclusive genes
by
matteo.levorato
• 0
thank you for your comment, but yes running DESeq2 is the starting point. dds <- DESeqDataSetFromMatrix(countData=RawCounts, …
Comment: Need help for downloading arabdopsis thaliana reference genome fasta file and gt
by
Ram
43k
Please stop pasting a sentence in the `tags` field. That field is for subject matter keywords. I've fixed your posts this time, please be m…
Comment: KEGG Pathways
by
Ram
43k
> is the below code correct Does it give you what you need?
Comment: from row count to tpm
by
Ram
43k
Hi https://www.biostars.org/u/119503/ Why did you delete this post?
Comment: ERROR When Using Ensembl Plants Biomart Wget API
by
GenoMax
141k
A couple of hours back using `plants.ensembl.org` was generating a 504 error but it seems to be working now. wget -O result.txt 'http…
Comment: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
Don't understand this comment. I don't have any columns with this name.
Answer: ERROR When Using Ensembl Plants Biomart Wget API
by
Ben_Ensembl
★ 2.4k
Hi Dora, For plant species such as *A. thalina*, you should use the http://plants.ensembl.org/biomart service, so the start of your wget…
Answer: Introduce SNPs on FASTA
by
christopher medway
▴ 450
You could take a look at the mutfa command in [seqtk][1] [1]: https://docs.csc.fi/apps/seqtk/#usage
Answer: Introduce SNPs on FASTA
by
Michael
54k
If you have a VCF file with all the ALT alleles that you need to insert and a reference genome in FASTA, you can use [bcftools consensus][1…
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