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Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 16 days ago by 40k • written 16 days ago by 157k
0
votes
1
reply
185
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 17 days ago by 77k • written 18 days ago by ▴ 30
4
votes
2
replies
2.3k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 25 days ago by 134k • written 3.4 years ago by 77k
0
votes
0
replies
246
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
5 weeks ago by Ming Tommy Tang ★ 3.4k
0
votes
0
replies
232
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
5 weeks ago by Ming Tommy Tang ★ 3.4k
13
votes
3
replies
11k
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 6 weeks ago by ▴ 20 • written 6.5 years ago by ★ 1.6k
5
votes
2
replies
453
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 6 weeks ago by 40k • written 6 weeks ago by ★ 2.4k
0
votes
0
replies
193
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
6 weeks ago by Ming Tommy Tang ★ 3.4k
9
votes
4
replies
4.0k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
7 weeks ago by Hamid Ghaedi 3.0k
6
votes
0
replies
220
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
6 weeks ago by barslmn ★ 1.8k
0
votes
0
replies
242
views
Tutorial: How to preprocess and visualize beautifully scRNA-seq with omicverse?
scRNA-seq seurat scanpy Python
7 weeks ago by Starlitnightly • 0
1
vote
0
replies
293
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 8 weeks ago by 40k • written 8 weeks ago by ★ 3.4k
3
votes
1
reply
316
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 9 weeks ago by 40k • written 9 weeks ago by 8.2k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 9 weeks ago by • 0 • written 7.6 years ago by 20k
1
vote
0
replies
320
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 10 weeks ago by 40k • written 10 weeks ago by ★ 3.4k
0
votes
0
replies
432
views
Tutorial: Differentially expressed gene analysis in Python with omicverse
RNA-seq Python
11 weeks ago by Starlitnightly • 0
19
votes
13
replies
6.8k
views
9 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 22 hours ago by 14k • written 15 months ago by 77k
2
votes
0
replies
2.7k
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 11 weeks ago by 40k • written 11 weeks ago by ★ 3.4k
18
votes
7
replies
5.7k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 10 weeks ago by 77k • written 3.5 years ago by 5.5k
3
votes
2
replies
470
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
10 weeks ago by Ming Tommy Tang ★ 3.4k
86
votes
22
replies
80k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 11 weeks ago by • 0 • written 5.2 years ago by ▴ 580
2
votes
0
replies
236
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 12 weeks ago by 40k • written 12 weeks ago by ★ 3.4k
4
votes
0
replies
356
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
3 months ago by Ming Tommy Tang ★ 3.4k
0
votes
0
replies
281
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 3 months ago by 40k • written 3 months ago by ★ 3.4k
0
votes
0
replies
306
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
3 months ago by sinha.shriprakash ▴ 20
1
vote
2
replies
479
views
Tutorial: How to ask computational biology questions
computational-biology
updated 3 months ago by 40k • written 3 months ago by ★ 3.4k
1
vote
0
replies
349
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 3 months ago by 40k • written 3 months ago by ★ 3.4k
2
votes
0
replies
334
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
3 months ago by Ming Tommy Tang ★ 3.4k
1
vote
0
replies
355
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
3 months ago by Ming Tommy Tang ★ 3.4k
0
votes
0
replies
390
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
3 months ago by Coremine Medical ▴ 10
1
vote
0
replies
367
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 3 months ago by 40k • written 3 months ago by ▴ 10
3
votes
0
replies
662
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
4 months ago by Ming Tommy Tang ★ 3.4k
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 4 months ago by 134k • written 9.9 years ago by 20k
2
votes
0
replies
732
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 6 months ago by 77k • written 6 months ago by ▴ 40
1
vote
0
replies
466
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine_learning papers scoring_function docking
6 months ago by Milad ▴ 10
3
votes
2
replies
2.4k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 4 months ago by 40k • written 6.4 years ago by ▴ 100
7
votes
3
replies
1.7k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 5 months ago by ▴ 110 • written 13 months ago by 86k
3
votes
3
replies
2.2k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 7 months ago by 40k • written 17 months ago by ★ 3.3k
1
vote
0
replies
730
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
8 months ago by firestar ★ 1.6k
11
votes
7
replies
1.7k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
6 months ago by barslmn ★ 1.8k
2
votes
1
reply
1.5k
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 8 months ago by 157k • written 8 months ago by ★ 1.8k
3
votes
2
replies
1.6k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
10 weeks ago by Dr.Animo ▴ 60
2
votes
0
replies
853
views
Tutorial: GEO data mining (III) - Gene pathway enrichment analysis with complete code sharing
geo R data-mining Gene-pathway-enrichment RNA-Seq
updated 3 months ago by 40k • written 9 months ago by ▴ 360
1
vote
0
replies
2.1k
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 3 months ago by 40k • written 9 months ago by ▴ 360
5
votes
0
replies
963
views
Tutorial: GEO data mining (IB) - Downloading Sequence Read Archive (SRA) raw data
geo RNA-Seq data-mining SRA
updated 3 months ago by 40k • written 9 months ago by ▴ 360
6
votes
0
replies
2.5k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
7 months ago by Novogene ▴ 360
50
votes
1
reply
7.4k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 7 months ago by 40k • written 3.0 years ago by 77k
1
vote
3
replies
695
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
6 months ago by barslmn ★ 1.8k
73
votes
60
replies
25k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 7 months ago by 40k • written 6.1 years ago by 86k
13
votes
31
replies
5.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 6 months ago by 40k • written 4.1 years ago by 8.2k
379 results • Page 1 of 8
Recent Votes
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
Comment: ncbi error report log for validate fastq issue
A: Bowtie2 MAPQ difference using local vs end-to-end alignment
C: Bowtie2 MAPQ difference using local vs end-to-end alignment
Answer: TPM RNA-seq data for differential expression analysis
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Recent Replies
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files by GenoMax 134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools) by Pierre Lindenbaum 157k
> My problem has been with trying to loop the process. ok here is a **nextflow** based solution,(NOT tested) workflow { …
Comment: Assessing Rockhopper's output by langziv ▴ 50
I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files by Pierre Lindenbaum 157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output by shelkmike ▴ 980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages by ATpoint 77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
Comment: Subclustering of intergated cells from scRNA-seq data by fifty_fifty ▴ 60
thank you. This is exactly what I was looking for
Answer: Search RCSB with a list of protein names? by Mensur Dlakic ★ 25k
This is not the most elegant solution, but it should work with previous suggestions. In this remote directory: http://ftp.wwpdb.org/p…
Answer: Automate the Splitting of a VCF File by Sample (bcftools) by Ram 40k
The manual says you can split samples out at once using the `+split` plugin. So, `bcftools +split -Oz -o <PATH> file.vcf.gz` should do the …
Comment: differences between trajectories in conditions with Monocle3 or other tools by Amitm ★ 2.2k
Phate (or Monocle) doesn't do UMAP. If you have done UMAP already (using seurat) then you could use the cell barcode to UMAP cluster label …
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Y • 0
I figured out how to make it work. The bams have to be comma separated not just by space: cd "${input_directory_with_associated_bam_fi…
Comment: Search RCSB with a list of protein names? by Joseph • 0
Hey, this is so close to what I'm looking for - I clarified in my edit. This is a great way to batch download lots of PDBs in RCSB by their…
Comment: Search RCSB with a list of protein names? by Joseph • 0
This is a really neat package, but I don't think it does exactly what I want, so I've clarified my question. This seems like it grabs a PD…
Comment: How to get the gft file to run velocyto for velocity analysis? by Chris ▴ 200
Yes, thank you! I figured it out but I got an error: velocyto run10x -m Hg38_rmsk.gtf WT/outs /cellranger/reference/refdata-cellranger…
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