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 : this year
all time
today
this week
this month
this year
128 results • Page
1 of 3
Sort: Views
Rank
Views
Votes
Replies
239
votes
176
replies
96k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 11 months ago by
Ram
43k • written 8.8 years ago by
TriS
★ 4.7k
93
votes
23
replies
93k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 3 months ago by
clara.apicella
• 0 • written 5.8 years ago by
otwtgin2010
▴ 610
150
votes
70
replies
51k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 8 months ago by
Raheleh
▴ 260 • written 6.5 years ago by
Kevin Blighe
88k
100
votes
106
replies
47k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 5 weeks ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
88k
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
90
votes
48
replies
34k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 6 months ago by
Ram
43k • written 10.6 years ago by
Irsan
★ 7.8k
84
votes
29
replies
32k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 9 months ago by
amziepickles
• 0 • written 8.2 years ago by
Obi Griffith
20k
73
votes
27
replies
28k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 5 months ago by
snardeli
• 0 • written 10.3 years ago by
Istvan Albert
100k
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 27 days ago by
Gordon
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
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
14
votes
3
replies
20k
views
Tutorial:
Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome
plot
coverage
samtools
updated 9 months ago by
William
▴ 30 • written 7.1 years ago by
kirannbishwa01
★ 1.6k
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
20 days ago by
Kevin Blighe
88k
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
83
votes
34
replies
19k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 11 months ago by
adelheidkratzer
• 0 • written 5.9 years ago by
egeulgen
★ 1.3k
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 8 weeks ago by
jkbonfield
★ 1.2k • written 5.2 years ago by
finswimmer
16k
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
65
votes
15
replies
15k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 11 months ago by
Ram
43k • written 5.6 years ago by
finswimmer
16k
11
votes
7
replies
14k
views
Tutorial:
Removing rows with duplicate values based on 1 or more key values - linux awk
awk
linux
bash
updated 12 months ago by
Ram
43k • written 6.7 years ago by
Kevin Blighe
88k
7
votes
13
replies
13k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
bcftools
updated 11 months ago by
Ram
43k • written 5.2 years ago by
jaybee
▴ 170
11
votes
7
replies
11k
views
Tutorial:
ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler
Software
rna-seq
updated 12 months ago by
Ram
43k • written 3.2 years ago by
Novogene
▴ 420
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 6 weeks ago by
Istvan Albert
100k • written 8.2 years ago by
Ram
43k
10
votes
31
replies
11k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 6 months ago by
ha2606
• 0 • written 6.3 years ago by
vimalkvn
▴ 320
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
21
votes
26
replies
9.7k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 8 weeks ago by
Yao
▴ 30 • written 4.4 years ago by
Juke34
8.6k
10
votes
1
reply
9.3k
views
Tutorial:
How to select reads with specific flag using samtools
next-gen-sequencing
updated 12 months ago by
Ram
43k • written 6.7 years ago by
imlituan
▴ 110
3
votes
2
replies
8.9k
views
Tutorial:
Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ
UMI
fastp
updated 12 months ago by
Ram
43k • written 6.5 years ago by
chen
★ 2.5k
3
votes
3
replies
8.8k
views
Tutorial:
High Speed Downloading of SRA, SAM and Fastq Files
fastq
sam
Aspera-Connect
sra
updated 12 months ago by
Ram
43k • written 6.4 years ago by
Wenhu_Cao
▴ 100
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
0
votes
0
replies
8.1k
views
Tutorial:
Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R
eviews
updated 12 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
15
votes
1
reply
7.2k
views
Tutorial:
A compilation of conversion tools for BED, SAM/BAM, psl, pslx, blast tabular and blast xml
psl
SAM
blast
BED
updated 12 months ago by
Ram
43k • written 6.5 years ago by
Joseph Hughes
★ 3.0k
6
votes
5
replies
7.0k
views
Tutorial:
use firehose_get to download TCGA data
tcga
RNA-Seq
updated 12 months ago by
Ram
43k • written 6.5 years ago by
jmzeng1314
▴ 140
2
votes
0
replies
6.9k
views
Tutorial:
How to - Install Python packages in a virtual environment (virtualenv)
ubuntu
cutadapt
virtualenv
python
windows
updated 12 months ago by
Ram
43k • written 6.4 years ago by
vimalkvn
▴ 320
19
votes
7
replies
6.6k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 10 months ago by
ATpoint
82k • written 4.1 years ago by
colindaven
6.4k
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
10
votes
4
replies
5.7k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
9 months ago by
Hamid Ghaedi
3.2k
6
votes
2
replies
5.0k
views
Tutorial:
Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
5 months ago by
GenoMax
142k
3
votes
4
replies
4.5k
views
Tutorial:
gencore: a tool to reduce sequencing noises by generating consensus reads
consensus
OpenGene
sequencing-noise
updated 11 months ago by
Ram
43k • written 6.0 years ago by
chen
★ 2.5k
10
votes
6
replies
4.2k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 7 weeks ago by
Ram
43k • written 6.2 years ago by
Kevin Blighe
88k
9
votes
9
replies
4.2k
views
Tutorial:
Determine % of reference genome covered by aligned SAM/BAM
reference-coverage
ngs
updated 12 months ago by
Ram
43k • written 6.7 years ago by
Kevin Blighe
88k
0
votes
0
replies
3.7k
views
Tutorial:
Park Test for Heteroskedasticity In R Commander
R
Park-Test
updated 12 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
3
votes
4
replies
3.6k
views
Tutorial:
Gene Set Enrichment Analysis on T-BioInfo
gene
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.5 years ago by
elia.brodsky
▴ 340
0
votes
0
replies
3.6k
views
Tutorial:
SFA (Stochastic Frontier Analysis) STATA 14
R
updated 12 months ago by
Ram
43k • written 6.3 years ago by
helgasaraswati
▴ 10
3
votes
1
reply
3.4k
views
Tutorial:
Affymetrix HTA 2.0 id conversion
biomart
HTA
affymetrix
Affymetrix
2.0
updated 3 months ago by
MaxF
▴ 120 • written 2.8 years ago by
Kevin Blighe
88k
1
vote
4
replies
3.4k
views
Tutorial:
Applying machine learning to NGS transcriptomic data
next-gen
RNA-Seq
updated 11 months ago by
Ram
43k • written 6.0 years ago by
elia.brodsky
▴ 340
2
votes
0
replies
3.3k
views
Tutorial:
use the tool slicer to split big files (like FASTQ) to smaller files for parallel processing
opengene
slicer
fastq
splitter
updated 11 months ago by
Ram
43k • written 6.6 years ago by
chen
★ 2.5k
2
votes
0
replies
3.2k
views
Tutorial:
How to read multiple matrices from GEO into R and make multiple Seurat objects and merge them into a single object.
unix
Seurat
single-cell
rstats
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
1
reply
3.2k
views
Tutorial:
Accessing sequences using batch entrez
genome
updated 12 months ago by
Ram
43k • written 6.6 years ago by
mawia.martha
• 0
0
votes
0
replies
3.1k
views
Tutorial:
Normality Test For JB (Jarque Bera) Test R Commander
Jarque-Bera-Test
R-Commander
updated 12 months ago by
Ram
43k • written 6.4 years ago by
helgasaraswati
▴ 10
7
votes
3
replies
3.0k
views
Tutorial:
Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation
rRNA
RNAmmer
Genome
updated 26 days ago by
colindaven
6.4k • written 16 months ago by
Dr.Animo
▴ 130
4
votes
2
replies
2.9k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 8 months ago by
GenoMax
142k • written 4.0 years ago by
ATpoint
82k
128 results • Page
1 of 3
Recent Votes
A: how to combine RNA seq data from 4 lanes
Answer: Cannot install bwa-mem2 via conda
Answer: Sub-sampling a BAM to a fixed number of reads
Comment: Downsample BAM file to specific amount of reads
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Answer: Long reads and fixing of mate-pair issues/marking duplicates with samtools
Answer: genome finishing
Recent Locations •
All
United States,
2 minutes ago
United States,
2 minutes ago
United States,
3 minutes ago
Frankrike,
4 minutes ago
Malta,
4 minutes ago
Belarus,
7 minutes ago
United States,
8 minutes ago
Recent Awards •
All
Scholar
to
rpolicastro
13k
Popular Question
to
Amr
▴ 160
Popular Question
to
asalimih
▴ 60
Popular Question
to
nd48
▴ 20
Scholar
to
Trivas
★ 1.8k
Popular Question
to
biology_inform
▴ 50
Popular Question
to
Joe
21k
Recent Replies
Comment: Wrong ZYGOSITY by ensembl vep on DeepVariant vcf file
by
asalimih
▴ 60
I found out that vep is only checking the GT field therefore assigning HOM to the Zygosity. Therefore the problem should be from deepvarian…
Comment: Add stats to boxplot in R
by
Lélé
• 0
To remove "Kruskall Wallis" you can try adding the argument label="p" or label = "p.signif" which displays the p-value or *** like this: …
Answer: Sequencing Depth (Read Depth) Calculations
by
GenoMax
142k
You could also use `pandepth` ([**LINK**][1]) or `mosdepth` ([**LINK**][2]) as well. These will allow you to be flexible about windowed cov…
Comment: Sequencing Depth (Read Depth) Calculations
by
Pierre Lindenbaum
161k
it looks looks ok to me. <!-- This cmd works and gives me 40.5235, I was wondering whether this cmd is right or wrong, and does anyone hav…
Comment: Add stats to boxplot in R
by
Ghada
• 0
Great. thats work. Do you know how can I remove the kruskall-Wallis name from the plot? Also I would like to draw a line under the kruskall…
Comment: Using ggplotly in R
by
jared.andrews07
★ 16k
Again, this is not particularly difficult to do with [plotly itself](https://plotly.com/r/line-and-scatter/#adding-color-and-size-mapping) …
Comment: Duplicated reads (IDs) from nanopore sequencing
by
GenoMax
142k
If you only have supplementary alignments then they may be caused by reasons mentioned here --> https://www.biostars.org/p/308853/ I did no…
Comment: Cannot install bwa-mem2 via conda
by
Pierre Lindenbaum
161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Answer: Cannot install bwa-mem2 via conda
by
Istvan Albert
100k
The problem is caused by running the ARM-based conda. Bioinformatics software is compiled for Intel based CPUs only. Uninstall that versio…
Comment: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
[https://www.biostars.org/p/9559284/][1] you could try this [1]: https://www.biostars.org/p/9559284/
Comment: Duplicated reads (IDs) from nanopore sequencing
by
marco.barr
▴ 110
it's also true that now I only have one pod5 folder, thanks anyway for clarifying the focus of the issue. Yes, they are probably secondary …
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
I'm unsure. I will say that looking for [ normalize](https://github.com/search?q=repo%3Atanaylab%2Fmetacells%20normalize&type=code) among t…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
Pierre Lindenbaum
161k
> Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the c…
Answer: genome finishing
by
nd48
▴ 20
What is the input? Do you have short reads (e.g. illumina 100bp paired reads)? As mentioned already, you already have the consensus i.e. c…
Comment: Circos Plot to Visualize Chromatin Accessibility Changes from ATAC-seq Data
by
biology_inform
▴ 50
I've been exploring different visualization tools like Circos and shinyCircos, and I've noticed that they require an input file similar to …
Traffic: 2794 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