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411 results • Page
2 of 9
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0
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0
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677
views
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
530
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
595
views
Tutorial:
Polygenic Risk Score Calculation
genetic-burden
r
prs
ggplot
glm
8 months ago by
barslmn
★ 2.1k
1
vote
0
replies
633
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
644
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
684
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 5 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
472
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
773
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
664
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
651
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
877
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
684
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
737
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
607
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
670
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
709
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
953
views
Tutorial:
How to make a heatmap in R and deep understand it
heatmap
r
11 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 11 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
817
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 2.0 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
953
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
1.5k
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
924
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
3.6k
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: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge
Answer: DNA methylation preprocessing
Comment: NGS forensics: how to know if data is fabricated
Answer: NGS forensics: how to know if data is fabricated
Comment: NGS forensics: how to know if data is fabricated
correcting for a batch in DESeq2
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Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I don't think people have undertaken the effort to create an anomaly detector for RNAseq -- people's efforts are dedicated towards developi…
Comment: NGS forensics: how to know if data is fabricated
by
dsull
★ 5.9k
I'd say post on pubpeer -- it's the best forum for this sort of discussion. As for what additional analysis I recommend: I'd say look at s…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> This is a super-interesting question from an algorithmic standpoint Ya, I was hoping to find some algorithm that would compare say a 're…
Comment: ScRNAseq-How to correctly choose cell type marker genes
by
Francesco
▴ 10
Thank you for your valuable suggestion!
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 520
> My first question would be how strong your background in such analysis > is. Very strong. PhD+several years working in the field. > Wot…
Comment: NGS forensics: how to know if data is fabricated
by
ATpoint
82k
My first question would be how strong your background in such analysis is. Claim of fabrication is very serious, so be 100% sure to back it…
Answer: NGS forensics: how to know if data is fabricated
by
Jeremy Leipzig
22k
This is a super-interesting question from an algorithmic standpoint (devising a model that can distinguish real from synthetic reads) but I…
Answer: absolute path for symbolic links in Snakefile
by
Jesse
▴ 740
It's nothing to do with Snakemake, just the ordinary confusion of making relative symlinks when your working directory is somewhere else. …
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
by
Jesse
▴ 740
[seqmagick](https://github.com/fhcrc/seqmagick/) has a `--squeeze-threshold` option that does just this. For example with an MSA of five s…
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by
Arup Ghosh
3.2k
Use the standalone version of Nextflow and specify the process-specific conda environments paths.
Comment: gvcf joint calling
by
Jeremy Leipzig
22k
can you show us an exonic position in your VCF file that is all `./.`?
Comment: Help understanding how KEGG Ortholog `K00004 ` has 3 ECs associated with it (EC:
by
O.rka
▴ 710
Thank you. This answers my question. The reason I am asking is because I’m trying to do set enrichment analysis with BRENDA pathways using…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
colindaven
6.4k
I used to use nextflow in a conda env. That requires the env to be active when a pipeline is started. Also I have productive pipelines whic…
Comment: different FeatureCounts output for the same data
by
Istvan Albert
100k
just to clarify, it is not that the program algorithm works differently but the meaning of the flags changed; before -p was sufficient to…
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Thanks Ram. Using merge maxed out my ram on a large list, but your suggestion directed me to purrr::reduce which works great.
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