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
348 results • Page
1 of 7
Sort: Rank
Rank
Views
Votes
Replies
76
votes
2
replies
50k
views
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
tutorial
Tutorial
written 9.0 years ago by
Eric Normandeau
11k
12
votes
5
replies
9.6k
views
6 follow
Tutorial:
Easy way to do GO enrichment in R
enrichr
gene
RNA-Seq
R
Tutorial
updated 6 weeks ago by
Kevin Blighe
81k • written 4.6 years ago by
ahmad mousavi
▴ 640
1
vote
0
replies
431
views
Tutorial:
Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
TCGA
Counts
v32.0
Biolinks
GDC
STAR
10 weeks ago by
dare_devil
★ 1.6k
29
votes
3
replies
6.5k
views
7 follow
Tutorial:
Methylation Analysis Tutorial in R_part1
Tutorial
cancer
methylation
R
updated 11 weeks ago by
GenoMax
117k • written 20 months ago by
Hamid Ghaedi
★ 2.5k
1
vote
2
replies
470
views
Tutorial:
Running fastq_screen on your data
fastqscreen
3 months ago by
rohitsatyam102
▴ 510
7
votes
12
replies
978
views
Tutorial:
Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 3 months ago by
Shred
▴ 640 • written 3 months ago by
thehung92phuyen
▴ 30
70
votes
14
replies
12k
views
15 follow
Tutorial:
List Of Bioinformatics Books
bioinformatics
tutorial
books
Tutorial
updated 4 months ago by
Paul A. Gagniuc
▴ 30 • written 9.1 years ago by
Medhat
9.3k
23
votes
13
replies
2.7k
views
9 follow
Tutorial:
How to get FASTQ reads from the Short Read Archive (SRA)
fastq
sra
updated 5 months ago by
liorglic
▴ 880 • written 8 months ago by
Istvan Albert
93k
3
votes
13
replies
6.7k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
merge
bcftools
Tutorial
written 3.3 years ago by
jaybee
▴ 140
12
votes
9
replies
1.9k
views
Tutorial:
TCGA transcriptome data to R (DESeq2)
TCGA
GDC
DESeq2
updated 13 days ago by
dk0319
▴ 30 • written 6 months ago by
Barry Digby
▴ 980
9
votes
0
replies
824
views
Tutorial:
Dealing with nanopore fast5 files compressed with vbz
hdf5
nanopore
fast5
vbz
MinKNOW
5 months ago by
dariober
13k
2
votes
0
replies
593
views
Tutorial:
Free Book : Computational Biology of a cell signalling pathway using R
cell
Biology
R
Computational
signalling
5 months ago by
sinha.shriprakash
▴ 20
0
votes
0
replies
2.7k
views
Tutorial:
Using PatMatch to search for nucleic and protein sequence patterns and integrate the results with Python/Jupyter for downstream analysis
Jupyter
Python
pattern
5 months ago by
Wayne
★ 1.2k
12
votes
4
replies
3.6k
views
Tutorial:
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
Tutorial
linux
bioinformatics
R
updated 6 months ago by
iamsmor
• 0 • written 16 months ago by
garden_giessen
▴ 120
21
votes
10
replies
37k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
Tutorial
error
software
R
updated 29 days ago by
Chih
• 0 • written 15 months ago by
Nitin Narwade
★ 1.2k
1
vote
0
replies
1.1k
views
Tutorial:
Unsupervised clustering on gene expression data
clustering
RNA-seq
expression
gene
3 months ago by
Hamid Ghaedi
★ 2.5k
35
votes
6
replies
12k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 5 months ago by
cameron.cowan
▴ 10 • written 15 months ago by
rpolicastro
8.8k
139
votes
67
replies
38k
views
17 follow
Tutorial:
Network plot from expression data in R using igraph
R
Tutorial
microarray
RNA-Seq
network
updated 8 months ago by
Hamtaro
▴ 10 • written 4.6 years ago by
Kevin Blighe
81k
122
votes
119
replies
23k
views
22 follow
Tutorial:
Survival analysis with gene expression
survival analysis
cox
geo
gene expression
Tutorial
6 weeks ago by
Kevin Blighe
81k
14
votes
1
reply
944
views
Tutorial:
Germline variant calling pipeline using Snakemake
snakemake
GATK
germline_variant_calling
updated 9 months ago by
dariober
13k • written 9 months ago by
nhaus
▴ 200
192
votes
47
replies
66k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
tutorial
bioconductor
microarray
analysis
tutorial
Tutorial
updated 4 months ago by
javanokendo
▴ 10 • written 9.7 years ago by
Obi Griffith
19k
20
votes
1
reply
1.7k
views
Tutorial:
Building Docker images
singularity
container
docker
9 months ago by
ATpoint
62k
6
votes
2
replies
717
views
Tutorial:
GSE28955 - Agilent-016436 Human miRNA Microarray 1.0
limma
GPL6955
Microarray
miRNA
Agilent
10 months ago by
Kevin Blighe
81k
0
votes
0
replies
644
views
Tutorial:
Alignment-free RNA-seq Differential Gene Expression Analysis with Kallisto & Sleuth
dge
kallisto
rnaseq
sleuth
10 months ago by
mo
• 0
1
vote
0
replies
851
views
Tutorial:
Affymetrix HTA 2.0 id conversion
biomart
HTA
affymetrix
Affymetrix
2.0
10 months ago by
Kevin Blighe
81k
45
votes
2
replies
34k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
tutorial
Tutorial
updated 11 months ago by
kjh98
• 0 • written 10.2 years ago by
MSU course 2011
▴ 540
86
votes
95
replies
28k
views
23 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial
1000
genomes
PCA
PLINK
updated 6 weeks ago by
dongxinyu510
• 0 • written 3.8 years ago by
Kevin Blighe
81k
70
votes
19
replies
9.3k
views
15 follow
Tutorial:
Gene Set Enrichment Analysis
enrichment
microarray
Tutorial
GSEA
RNA-Seq
8 weeks ago by
Hamid Ghaedi
★ 2.5k
0
votes
0
replies
513
views
Tutorial:
Event & tutorial: open software tools and AI for improving bioimaging (SLURM, containerisation)
containerisation
bioimaging
SLURM
health
12 months ago by
Erin Haskell | ELIXIR
▴ 460
1
vote
0
replies
700
views
Tutorial:
Slurm and parallelization
slurm
12 months ago by
Juke34
★ 7.1k
1
vote
0
replies
615
views
Tutorial:
How to: make Camellia sinensis var. sinensis (black tea) custom annotation files for BINGO Cytoscape
bingo
cytoscape
12 months ago by
Pratik
▴ 770
12
votes
1
reply
1.3k
views
Tutorial:
PCR Primer or Primer+Probe design
pcr
probe
rt-pcr
qpcr
primer
updated 12 months ago by
jared.andrews07
★ 13k • written 12 months ago by
Kevin Blighe
81k
113
votes
66
replies
35k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
ENA
Fastq
Tutorial
11 months ago by
ATpoint
62k
4
votes
0
replies
641
views
Tutorial:
Long Read Genome Assembly Video Series
long-read
genome-assembly
12 months ago by
pbpanigrahi
▴ 410
0
votes
1
reply
504
views
Tutorial:
Add Customized Filters in GDC
gdc
updated 12 months ago by
cpad0112
20k • written 12 months ago by
Zhenyu Zhang
▴ 540
61
votes
26
replies
8.4k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
bam
consensus
fasta
Tutorial
updated 12 months ago by
bioinfo8
▴ 180 • written 3.3 years ago by
finswimmer
15k
11
votes
20
replies
9.5k
views
10 follow
Tutorial:
Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat
single cell
RNA-Seq
TCR
Tutorial
13 months ago by
jared.andrews07
★ 13k
4
votes
2
replies
1.6k
views
Tutorial:
Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle 5.0
Tutorial
updated 13 months ago by
GenoMax
117k • written 3.0 years ago by
Shicheng Guo
★ 9.1k
32
votes
13
replies
30k
views
9 follow
Tutorial:
Using R in Conda
R
Tutorial
updated 3 months ago by
Siddharth
• 0 • written 23 months ago by
rohitsatyam102
▴ 510
31
votes
9
replies
16k
views
11 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
Tutorial
updated 29 days ago by
Verónica
• 0 • written 22 months ago by
lavinia.gordon
▴ 140
98
votes
16
replies
27k
views
18 follow
Tutorial:
Heatmaps in R
Tutorial
R
heatmap
7 weeks ago by
Jean-Karim Heriche
25k
18
votes
1
reply
2.1k
views
Tutorial:
Extracting genomic feature sequences from GTF/GFF files with AGAT
extract
GTF
GFF
sequence
updated 14 months ago by
Michael Dondrup
51k • written 14 months ago by
Juke34
★ 7.1k
31
votes
6
replies
6.3k
views
Tutorial:
A simple tutorial for a complex ComplexHeatmap
complexheatmap
clustering
arthritis
pam
Tutorial
10 months ago by
Kevin Blighe
81k
75
votes
40
replies
25k
views
23 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 3 months ago by
Ram
36k • written 8.7 years ago by
Irsan
★ 7.5k
8
votes
0
replies
1.5k
views
Tutorial:
Pipes in R: An introduction and some advanced tips and tricks.
R
15 months ago by
rpolicastro
8.8k
233
votes
176
replies
78k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
TCGA
Survival
Tutorial
updated 3 months ago by
Ram
36k • written 6.9 years ago by
TriS
★ 4.5k
6
votes
0
replies
939
views
Tutorial:
data.frames in R: How vectorization can save you time and heartache
R
15 months ago by
rpolicastro
8.8k
8
votes
1
reply
741
views
Tutorial:
Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk
fasta
Tutorial
15 months ago by
Kevin Blighe
81k
15
votes
9
replies
3.2k
views
Tutorial:
Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R
tidyverse
gene
Tutorial
updated 9 months ago by
krushnach80
★ 1.1k • written 22 months ago by
rpolicastro
8.8k
12
votes
2
replies
816
views
Tutorial:
Factors in R - How do they work, and how did I break my data?
R
Tutorial
15 months ago by
rpolicastro
8.8k
348 results • Page
1 of 7
Recent Votes
VQSR bias against rare variants
Answer: pymol for superimpose by python script
Comment: aligner for CORRECTED pacbio long reads
How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
A: How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
Comment: How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
Recent Locations •
All
United States,
just now
United States,
1 minute ago
United States,
2 minutes ago
Bologna,
2 minutes ago
United States,
5 minutes ago
United States,
7 minutes ago
Canada,
13 minutes ago
Recent Awards •
All
Popular Question
to
predeus
★ 1.8k
Scholar
to
rpolicastro
8.8k
Scholar
to
GenoMax
117k
Popular Question
to
bioinformatics.queries
▴ 50
Popular Question
to
ieie
▴ 10
Scholar
to
chrchang523
9.3k
Teacher
to
jockbanan
▴ 420
Recent Replies
Comment: analyzing a single cell and searching for a specific gene using single cell data
by
Bioinfo
• 0
@rpolicastro yes they do have the h5ad data but I cannot figure how to make a use out of it. It seems they just cluster things and that is …
Comment: pymol for superimpose by python script
by
iamsmor
• 0
Thank you so much, you really wonderful person, spend your time for long detailed explaination.
Answer: Problem using FastML for ancestral sequence reconstruction
by
Mensur Dlakic
★ 19k
It does not seem that you understand the meaning of this error message: > sh: 1: cannot create outdir/fastml.std: Directory nonexistent …
Comment: aligner for CORRECTED pacbio long reads
by
gconcepcion
▴ 280
This is a very old and outdated link, what is it exactly that you are trying to do? Align PacBio HiFi reads to a reference? Try minimap…
Comment: How To Do Alignment, Stop Codon Removal And Dn/Ds Calulation In One Go?
by
sunnykevin97
▴ 760
You have to use the nucleotide (CDS) alignment file as input.
Comment: What Is Ad (Allelic Depth) In 1000Genomes Vcf?
by
Maryam
• 0
Hello, This post is so helpful. My question is according to quality scoring of variants, the good AD threshold should be >8. Then how…
Comment: Incomplete alignment EMBOSS needleall
by
lieven.sterck
14k
not sure if it takes fastq as input (though yes, there example on their site is named .fastq , but when you look at that file it is a fasta…
Comment: Extract sequence from Fasta using header
by
GenoMax
117k
@princy: You have asked many questions on biostars over the last few months but appear not to have validated any of them. Accepting answers…
Answer: Extract sequence from Fasta using header
by
lieven.sterck
14k
`seqkit` will be able to do this. (subprogram `seq` ) (alternative, if you have a blastdb of that fasta file, you can also get them by u…
Answer: Extract sequence from Fasta using header
by
GenoMax
117k
See: https://www.biostars.org/p/434016/#434038
Comment: Best pipeline for RNAseq assembly and analysis (or help with stringtie assembly)
by
Katherine
• 0
I thought that the file I used was the most up to date. Here is the header of the file: gff-version 3 !gff-spec-version 1.21 !processor…
Comment: analyzing a single cell and searching for a specific gene using single cell data
by
rpolicastro
8.8k
They provide an h5ad file, which may contain the already processed data, plus associated cell and feature metadata. If so, you should load …
Answer: Extract header from fasta file
by
cpad0112
20k
$ awk -F "_|:" -v OFS="_" '/^>/{print ">"$2,$3,$4,$5,$6};!/>/' test.fa >TRINITY_DN74698_c0_g1_i1 MRIRSVVFTLRPRAKWMAPSSGMRL…
Answer: analyzing a single cell and searching for a specific gene using single cell data
by
jared.andrews07
★ 13k
I'd recommend you read what goes into a single cell analysis. The [Orchestrating Single Cell Analysis](http://bioconductor.org/books/releas…
Answer: Extract header from fasta file
by
rpolicastro
8.8k
A [seqkit](https://bioinf.shenwei.me/seqkit/) answer. You may need to tweak the regex depending on the variability in the naming scheme. `…
Traffic: 1078 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