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411 results • Page
2 of 9
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0
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0
replies
678
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Tutorial:
T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq
TCR
single-cell
computational
biology
8 months ago by
Ming Tommy Tang
★ 3.9k
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 7.1 years ago by
kirannbishwa01
★ 1.6k
8
votes
2
replies
1.1k
views
Tutorial:
Updated List of Unix tutorials 2023
Unix
updated 8 months ago by
Ram
43k • written 8 months ago by
carlopecoraro2
★ 2.5k
1
vote
0
replies
535
views
Tutorial:
cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome
rstats
spatial
single-cell
8 months ago by
Ming Tommy Tang
★ 3.9k
9
votes
4
replies
5.5k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
8 months ago by
Hamid Ghaedi
3.2k
7
votes
0
replies
597
views
Tutorial:
Polygenic Risk Score Calculation
genetic-burden
r
prs
ggplot
glm
8 months ago by
barslmn
★ 2.1k
1
vote
0
replies
636
views
Tutorial:
common mistakes in using spreadsheets
excel
spreadsheet
structured-data
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
3
votes
1
reply
645
views
Tutorial:
Coordinate Systems and genomic variant description
coordinate-system
HGVS
normalization
VCF
updated 9 months ago by
Ram
43k • written 9 months ago by
Juke34
8.5k
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 8.1 years ago by
Obi Griffith
20k
1
vote
0
replies
685
views
Tutorial:
How to convert gene ids in R
computational-biology
gene-id
rstats
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
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
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 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
19
votes
7
replies
6.6k
views
Tutorial:
scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count
scRNA-seq
RNA-Seq
updated 9 months ago by
ATpoint
82k • written 4.1 years ago by
colindaven
6.4k
4
votes
2
replies
1.1k
views
Tutorial:
How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC
transcription
factor
ChIP-seq
9 months ago by
Ming Tommy Tang
★ 3.9k
93
votes
23
replies
92k
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
2
votes
0
replies
476
views
Tutorial:
Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering
gene-expression
rstats
updated 9 months ago by
Ram
43k • written 9 months ago by
Ming Tommy Tang
★ 3.9k
4
votes
0
replies
777
views
Tutorial:
How to do GSEA in R for RNAseq data
gsea
RNAseq
rstats
10 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
667
views
Tutorial:
How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq
rstats
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
653
views
Tutorial:
Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling
R
Computational-Biology
10 months ago by
sinha.shriprakash
▴ 20
1
vote
2
replies
882
views
Tutorial:
How to ask computational biology questions
computational-biology
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
685
views
Tutorial:
How to pre-process scRNAseq data from fastq to count matrix with two lines of code
unix
scRNA-seq
single-cell
rstats
updated 10 months ago by
Ram
43k • written 10 months ago by
Ming Tommy Tang
★ 3.9k
3
votes
0
replies
740
views
Tutorial:
best practices for single-cell RNAseq analysis
cell
single
scRNAseq
10 months ago by
Ming Tommy Tang
★ 3.9k
1
vote
0
replies
609
views
Tutorial:
How to make a perfect heatmap using RNAseq data
heatmap
RNAseq
rstats
10 months ago by
Ming Tommy Tang
★ 3.9k
0
votes
0
replies
672
views
Tutorial:
How to start disease research quickly and easily?
proteins
pathways
disease
research-design
genes
10 months ago by
Coremine Medical
▴ 20
2
votes
0
replies
712
views
Tutorial:
Get a list of genes associated with a drug in 1 min
drug
genes
drug-targets
updated 10 months ago by
Ram
43k • written 10 months ago by
Coremine Medical
▴ 20
4
votes
0
replies
954
views
Tutorial:
How to make a heatmap in R and deep understand it
heatmap
r
12 months ago by
Ming Tommy Tang
★ 3.9k
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
2
votes
0
replies
1.0k
views
Tutorial:
ChIP-Seq Analysis Tutorial
Epigenetics
Bowtie2
MACS2
ChIP-Seq
Motif
updated 13 months ago by
ATpoint
82k • written 13 months ago by
Simon
▴ 40
1
vote
0
replies
819
views
Tutorial:
List of Machine Learning-Based Scoring Function Papers
machine-learning
docking
papers
updated 5 months ago by
Ram
43k • written 13 months ago by
Milad
▴ 10
3
votes
2
replies
2.7k
views
Tutorial:
Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences
Workshops
updated 11 months ago by
Ram
43k • written 7.0 years ago by
jnowacki
▴ 100
7
votes
3
replies
2.5k
views
Tutorial:
Automated dbSNP lookup by rsID position, plus genome build liftover
rsid
hg19
liftover
hg38
dbsnp
updated 12 months ago by
Randy H
▴ 110 • written 20 months ago by
Kevin Blighe
87k
3
votes
3
replies
2.8k
views
Tutorial:
Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC
TCGABiolinks
STAR
updated 14 months ago by
Ram
43k • written 2.1 years ago by
DareDevil
★ 4.3k
2
votes
0
replies
1.2k
views
Tutorial:
Analysis of Smart-Seq3 data with kallisto-bustools
single-cell
kallisto
transcriptomics
smart-seq3
pipeline
updated 5 months ago by
Ali
• 0 • written 15 months ago by
firestar
★ 1.6k
11
votes
7
replies
2.3k
views
Tutorial:
Sequence Alignment from Scratch with BWA
alignment
bwa
DNA
13 months ago by
barslmn
★ 2.1k
2
votes
1
reply
2.7k
views
Tutorial:
Converting TSV file to VCF
vcf
preprocessing
frequency
updated 15 months ago by
Pierre Lindenbaum
161k • written 15 months ago by
barslmn
★ 2.1k
2
votes
0
replies
1.2k
views
Tutorial:
GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo
R
data-mining
Gene-pathway-enrichment
RNA-Seq
updated 10 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
1
vote
0
replies
2.6k
views
Tutorial:
GEO Data Mining (II) - Differential gene expression analysis and visualization with complete code sharing
geo
R
data-mining
differential-gene-expression
RNA-Seq
updated 10 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
5
votes
0
replies
1.6k
views
Tutorial:
GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo
RNA-Seq
data-mining
SRA
updated 10 months ago by
Ram
43k • written 16 months ago by
Novogene
▴ 420
6
votes
0
replies
5.4k
views
Tutorial:
How to download GEO data Quickly and easily
geo
RNA-Seq
R
data-mining
14 months ago by
Novogene
▴ 420
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
1
vote
3
replies
956
views
Tutorial:
Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo
DNA
motif
gibbssampling
splice
13 months ago by
barslmn
★ 2.1k
73
votes
60
replies
27k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 14 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
14
votes
31
replies
6.8k
views
6 follow
Tutorial:
gene set filter/selection for training ab initio annotation tools
geneset
genome
gene
abinitio
updated 13 months ago by
Ram
43k • written 4.7 years ago by
Juke34
8.5k
1
vote
2
replies
1.6k
views
Tutorial:
ViennaRNA package installation in Windows
windows
rna
mfold
viennarna
updated 10 months ago by
Ram
43k • written 19 months ago by
Sandhiya
▴ 20
1
vote
0
replies
927
views
Tutorial:
Making LDA Score plot
LDA
metagenomics
19 months ago by
rohitsatyam102
▴ 850
133
votes
123
replies
38k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 13 months ago by
1769mkc
★ 1.2k • written 5.5 years ago by
Kevin Blighe
87k
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 3.2 years ago by
Novogene
▴ 420
15
votes
1
reply
4.0k
views
Tutorial:
Dealing with nanopore fast5 files compressed with vbz
hdf5
nanopore
fast5
vbz
MinKNOW
updated 20 months ago by
Assa Yeroslaviz
★ 1.8k • written 2.3 years ago by
dariober
14k
28
votes
0
replies
3.7k
views
Tutorial:
Building Docker images
singularity
docker
container
21 months ago by
ATpoint
82k
2
votes
1
reply
60k
views
Tutorial:
Docker denied: requested access to the resource is denied
docker
updated 21 months ago by
LauferVA
4.2k • written 21 months ago by
kodwings
▴ 20
411 results • Page
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Recent Votes
Comment: MA plot of shrunken fold change
Answer: Single-stranded RNA-seq: strandedness of samples
Comment: NGS forensics: how to know if data is fabricated
Answer: blasting genome contigs against local SILVA 16S RNA database
blasting genome contigs against local SILVA 16S RNA database
Comment: Integrate transcriptomic data and proteomics data.
Comment: MA plot of shrunken fold change
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Recent Replies
Answer: Taking the difference of two VCFs (or removing singletons)
by
Andres
▴ 20
I know this is an old question but when searching for filtering out singletons(and doubletons too) i found this post in the first results. …
Comment: NGS forensics: how to know if data is fabricated
by
i.sudbery
19k
In which case, I'd definately look at the distribution of read lengths, post trimming, and see if there is a discontinuity in the distribut…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
I would note that even on a good, polyA selected, RNA-seq run, I would only expect 60-75% of mapped reads to map to protein coding exons.
Answer: FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last plac
by
David Langenberger
11k
:: FINAL CALL :: 8th Berlin Summer School in NGS Data Analysis 2024 - Only a few last places available
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Oh, then I will check the output file from featureCounts.
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
How would I check if these reads are aligning to regions where there is no expressed sequence know? Should I follow the suggestion of i.sud…
Answer: Deseq2
by
Jack Tierney
▴ 360
[This vignette][1] is a great place to start. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.ht…
Comment: Genbank File Format
by
alenew.am
• 0
Thanks, yes i have tried first here looking for a easier solution (for me), i didnt' know if this format was already available somewhere. t…
Comment: Genbank File Format
by
alenew.am
• 0
Yes, it would be fine with an external solution, thanks for the reply
Answer: Polishing genome assembly
by
Michael
54k
If you have Hifi reads your error rate should already be quite good, therefore polishing with potentially longer and slightly more error-pr…
Comment: Integrate transcriptomic data and proteomics data.
by
Lluís R.
★ 1.2k
You don't need to subset for common features, there are tools that work for that like RGCCA, mixOmics. See for instance a classification [h…
Answer: Integrate transcriptomic data and proteomics data.
by
KABILAN
▴ 50
You can use R package named 'mixOmics' to integrate the datasets. Kindly go through the manual of this package.
Comment: Need help for downloading arabdopsis thaliana reference genome fasta file and gt
by
Michael
54k
You will have to describe your problem in much more detail, we are unable to understand what the problem even is. > Please, anyone, sugge…
Comment: MA plot of shrunken fold change
by
Sudip
• 0
Thank you.
Comment: MA plot of shrunken fold change
by
ATpoint
82k
You will need to relevel to make all comparisons available as coefficients, see https://www.biostars.org/p/448959/, or just use ashr shrink…
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