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140 results • Page
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239
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176
replies
94k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 10 months ago by
Ram
43k • written 8.7 years ago by
TriS
★ 4.7k
98
votes
106
replies
46k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 9 days ago by
psb7
▴ 20 • written 5.6 years ago by
Kevin Blighe
87k
149
votes
70
replies
50k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 7 months ago by
Raheleh
▴ 260 • written 6.4 years ago by
Kevin Blighe
87k
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 5 months ago by
Ram
43k • written 10.5 years ago by
Irsan
★ 7.8k
83
votes
34
replies
18k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 10 months ago by
adelheidkratzer
• 0 • written 5.8 years ago by
egeulgen
★ 1.3k
10
votes
31
replies
11k
views
10 follow
Tutorial:
OrthoMCL installation on Ubuntu Linux
ubuntu
orthomcl
mysql
linux
updated 5 months ago by
ha2606
• 0 • written 6.3 years ago by
vimalkvn
▴ 320
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 20 days ago by
Istvan Albert
100k • written 8.1 years ago by
Ram
43k
70
votes
29
replies
15k
views
13 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 5 weeks ago by
jkbonfield
★ 1.2k • written 5.1 years ago by
finswimmer
16k
84
votes
29
replies
32k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 8 months ago by
amziepickles
• 0 • written 8.1 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 4 months ago by
snardeli
• 0 • written 10.2 years ago by
Istvan Albert
100k
21
votes
26
replies
9.5k
views
11 follow
Tutorial:
Create de novo repeat library
de-novo
repeat
annotation
updated 4 weeks ago by
Yao
▴ 30 • written 4.4 years ago by
Juke34
8.5k
85
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 10 hours ago by
Gordon
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
93
votes
23
replies
91k
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 5.7 years ago by
otwtgin2010
▴ 610
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 11 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 4 weeks ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
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
141k • written 3.7 years ago by
lavinia.gordon
▴ 160
65
votes
15
replies
14k
views
Tutorial:
Which human reference genome should I use?
assembly
genome
alignment
updated 10 months ago by
Ram
43k • written 5.5 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 5 weeks ago by
Konstantinos
• 0 • written 3.5 years ago by
Hamid Ghaedi
3.2k
21
votes
13
replies
10k
views
10 follow
Tutorial:
Setting up Aspera Connect (ascp) on Linux and macOS
ascp
aspera
updated 5 months ago by
jude
• 0 • written 21 months ago by
ATpoint
81k
18
votes
13
replies
2.2k
views
Tutorial:
Screen shots of text (please don't)!
meta
updated 11 months ago by
Ram
43k • written 7.1 years ago by
Michael
54k
7
votes
13
replies
13k
views
Tutorial:
Merging multiple vcf files into Single vcf file
vcf
bcftools
updated 10 months ago by
Ram
43k • written 5.2 years ago by
jaybee
▴ 170
12
votes
11
replies
7.5k
views
Tutorial:
How to upload your RNA-Seq data to NCBI Sequence Read Archive (SRA)
NCBI
Bioproject
SRA
BioSample
updated 11 months ago by
Ram
43k • written 7.1 years ago by
CandiceChuDVM
★ 2.4k
9
votes
9
replies
4.2k
views
Tutorial:
Determine % of reference genome covered by aligned SAM/BAM
reference-coverage
ngs
updated 11 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
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 11 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
19
votes
7
replies
6.5k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 9 months ago by
ATpoint
81k • written 4.1 years ago by
colindaven
6.3k
11
votes
7
replies
11k
views
Tutorial:
ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler
Software
rna-seq
updated 11 months ago by
Ram
43k • written 3.1 years ago by
Novogene
▴ 410
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 6.6 years ago by
steve
★ 3.5k
10
votes
6
replies
4.1k
views
Tutorial:
CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation
corlevelplot
updated 22 days ago by
Ram
43k • written 6.2 years ago by
Kevin Blighe
87k
1
vote
5
replies
591
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq
TOSICA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
5
votes
5
replies
6.9k
views
Tutorial:
use firehose_get to download TCGA data
tcga
RNA-Seq
updated 11 months ago by
Ram
43k • written 6.4 years ago by
jmzeng1314
▴ 130
9
votes
5
replies
2.3k
views
Tutorial:
What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 11 months ago by
Ram
43k • written 6.8 years ago by
Istvan Albert
100k
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
1
vote
4
replies
3.3k
views
Tutorial:
Applying machine learning to NGS transcriptomic data
next-gen
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.9 years ago by
elia.brodsky
▴ 340
0
votes
4
replies
708
views
Tutorial:
Reverse pharmacology: how to predict drugs with genes or disease names?
drugs
drug-targets
genes
5 months ago by
Coremine Medical
▴ 20
3
votes
4
replies
3.6k
views
Tutorial:
Gene Set Enrichment Analysis on T-BioInfo
gene
RNA-Seq
updated 10 months ago by
Ram
43k • written 5.5 years ago by
elia.brodsky
▴ 340
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
9
votes
4
replies
5.4k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
8 months ago by
Hamid Ghaedi
3.2k
3
votes
3
replies
8.7k
views
Tutorial:
High Speed Downloading of SRA, SAM and Fastq Files
fastq
sam
Aspera-Connect
sra
updated 11 months ago by
Ram
43k • written 6.3 years ago by
Wenhu_Cao
▴ 100
2
votes
3
replies
2.7k
views
Tutorial:
It's about the journey, and not the destination
R
network
updated 11 months ago by
Ram
43k • written 7.0 years ago by
theobroma22
★ 1.2k
2
votes
3
replies
531
views
Tutorial:
Bulk RNA-seq: Different Expression Analysis with DEseq2
python
pyDESeq2
RNA-seq
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
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 8 months ago by
William
▴ 30 • written 7.0 years ago by
kirannbishwa01
★ 1.6k
3
votes
3
replies
1.1k
views
Tutorial:
multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation
RNAseq
multiomics
updated 3 months ago by
sil_bioinfo
▴ 40 • written 7 months ago by
Ming Tommy Tang
★ 3.9k
3
votes
2
replies
8.8k
views
Tutorial:
Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ
UMI
fastp
updated 11 months ago by
Ram
43k • written 6.4 years ago by
chen
★ 2.5k
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
4 months ago by
GenoMax
141k
1
vote
2
replies
866
views
Tutorial:
How to ask computational biology questions
computational-biology
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
4
votes
2
replies
2.8k
views
Tutorial:
Building mosdepth on macOS
nim
mosdepth
updated 7 months ago by
GenoMax
141k • written 3.9 years ago by
ATpoint
81k
3
votes
2
replies
3.9k
views
Tutorial:
Galaxy Tutorial on ChIP-seq
galaxy
ChIP-Seq
updated 11 months ago by
Ram
43k • written 7.0 years ago by
anton
▴ 30
3
votes
2
replies
511
views
Tutorial:
Single-cell RNA-seq: Preprocessing: Data integration and batch correction-2
scRNA-seq
updated 3 months ago by
ATpoint
81k • written 3 months ago by
Julia Ma
▴ 120
10
votes
2
replies
3.7k
views
Tutorial:
Graph visualization with igraph in R
Visualization
igraph
Graph
R
Network
updated 11 months ago by
Ram
43k • written 7.0 years ago by
Jean-Karim Heriche
27k
20
votes
2
replies
8.0k
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
140 results • Page
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Answer: Assume "yes" as the answer to any prompts with bioconda
Answer: Assume "yes" as the answer to any prompts with bioconda
Comment: biomaRt error for different R version
Answer: What is the normalization status of metabric data?
Answer: Assume "yes" as the answer to any prompts with bioconda
Answer: Assume "yes" as the answer to any prompts with bioconda
Answer: biomaRt error for different R version
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Answer: DEseq2
by
ATpoint
81k
The DESeq2 input is a numeric count matrix (or data.frame) with rows being genes/observations and columns being samples/cells/specimen. Ple…
Comment: How to add motifs in cellranger-arc reference?
by
Ehsan
• 0
Hi. Do you have any updates on what you ended up doing? I am encountering same issue, cannot really find a good TF motif database for zebra…
Comment: biomaRt error for different R version
by
manaswwm
▴ 490
Wonderful, and thanks for tagging Mike! For those who come back for this problem, the following seemed to work for me: Downgrading `dbply…
Answer: Assume "yes" as the answer to any prompts with bioconda
by
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8.5k
From my experience using `biocontainers` base container no need to set `yes` installation is done without any command prompt, otherwise as …
Comment: SLURM submission problem: Indexing the Reference Genome is not done in STAR
by
Dave Carlson
★ 1.7k
You're allocating 4 compute nodes (`#SBATCH -N 4`), but STAR can't actually make use of more than 1 compute node. You can increase the num…
Answer: Assume "yes" as the answer to any prompts with bioconda
by
Dave Carlson
★ 1.7k
```conda install -y bioconda::packageX conda-forge::packageY``` should do what you're looking for.
Comment: Supergnova stuck in tutorial
by
Murat
• 0
Hi GenoMax, Thank you for your advice. I sent an email to them and have already opened an issue on Github. Let see if there is any other so…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
You can't. The data does not exist. UniProt only annotates where a lysine is know to be acetylated. There is no way that UniProt can know w…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Jacky
• 0
Yes, that's what I meant.
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
Jacky
• 0
I'm sorry, I didn't explain it clearly. Below are my operational steps: I enter 'Triticum aestivum' in the search box and perform a search.…
Comment: Indexing the Reference Genome is not done in STAR
by
n_navy
• 0
I add these parameters; #SBATCH -N 4 #SBATCH --tasks=1 #SBATCH -c 4 #SBATCH --time=24:00:00 But it keeps giving error
Comment: RNA seq differential expression analysis
by
rrehimi
• 0
Thanks! Could you please explain the DEseq2 method using Galaxy step by step? Input files?
Answer: Korean reference file
by
colindaven
6.3k
Is is this one - KOREF ? There might be multiple versions. https://www.ncbi.nlm.nih.gov/bioproject/PRJNA294231/ If it is, then take that…
Comment: How can I retrieve wheat lysine non-acetylated sequences from the UniProt databa
by
me
▴ 750
The question is not quite clear? are you asking for wheat proteins in UniProtKB which contain a lysine amino-acid, where those lysine are *…
Comment: RNA seq differential expression analysis
by
seta
★ 1.9k
You should provide row count (without normalization) for doing DEG analysis by relevant tools such as, edgeR or DEseq.
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