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411 results • Page 2 of 9
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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 ▴ 30 • written 7.1 years ago by ★ 1.6k
8
votes
2
replies
1.1k
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 8 months ago by 43k • written 8 months ago by ★ 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 43k • written 9 months ago by ★ 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 43k • written 9 months ago by 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 • 0 • written 8.1 years ago by 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 43k • written 9 months ago by ★ 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 • 0 • written 22 months ago by 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 43k • written 9 months ago by ★ 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 82k • written 4.1 years ago by 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 • 0 • written 5.8 years ago by ▴ 610
2
votes
0
replies
477
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 9 months ago by 43k • written 9 months ago by ★ 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
668
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 10 months ago by 43k • written 10 months ago by ★ 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 43k • written 10 months ago by ★ 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 43k • written 10 months ago by ★ 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 43k • written 10 months ago by ▴ 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 141k • written 10.4 years ago by 20k
2
votes
0
replies
1.0k
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 13 months ago by 82k • written 13 months ago by ▴ 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 43k • written 13 months ago by ▴ 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 43k • written 7.0 years ago by ▴ 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 ▴ 110 • written 20 months ago by 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 43k • written 2.1 years ago by ★ 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 • 0 • written 15 months ago by ★ 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 161k • written 15 months ago by ★ 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 43k • written 16 months ago by ▴ 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 43k • written 16 months ago by ▴ 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 43k • written 16 months ago by ▴ 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 43k • written 3.6 years ago by 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 43k • written 6.6 years ago by 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 43k • written 4.7 years ago by 8.5k
1
vote
2
replies
1.6k
views
Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 10 months ago by 43k • written 19 months ago by ▴ 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 ★ 1.2k • written 5.5 years ago by 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 43k • written 3.2 years ago by ▴ 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 ★ 1.8k • written 2.3 years ago by 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 4.2k • written 21 months ago by ▴ 20
411 results • Page 2 of 9
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
Comment: unable to get feature count results by GenoMax 141k
Galaxy specific questions are best posted to their support site: https://help.galaxyproject.org/ That said, problems with counting are lik…
Comment: Landmark gene selection in L1000. by GenoMax 141k
Link for the data is included above.
Comment: Introduce SNPs on FASTA by GenoMax 141k
If you have specific changes you want to make then you can edit the fasta file accordingly.
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.
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