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Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 13 days ago by 40k • written 13 days ago by 157k
0
votes
1
reply
180
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 14 days ago by 76k • written 14 days ago by ▴ 30
4
votes
2
replies
2.3k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 21 days ago by 134k • written 3.4 years ago by 76k
0
votes
0
replies
235
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
4 weeks ago by Ming Tommy Tang ★ 3.4k
0
votes
0
replies
230
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 5 weeks ago by ▴ 20 • written 6.5 years ago by ★ 1.6k
4
votes
2
replies
441
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 5 weeks ago by 40k • written 5 weeks ago by ★ 2.3k
0
votes
0
replies
189
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
6 weeks ago by Hamid Ghaedi 3.0k
6
votes
0
replies
217
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
6 weeks ago by barslmn ★ 1.8k
0
votes
0
replies
232
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
288
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
312
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 8 weeks ago by 40k • written 8 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
313
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
425
views
Tutorial: Differentially expressed gene analysis in Python with omicverse
RNA-seq Python
10 weeks ago by Starlitnightly • 0
18
votes
13
replies
6.7k
views
9 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
aspera ascp
updated 10 weeks ago by 53k • written 15 months ago by 76k
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 10 weeks ago by 40k • written 10 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 76k • written 3.5 years ago by 5.5k
3
votes
2
replies
468
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
231
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 11 weeks ago by 40k • written 11 weeks ago by ★ 3.4k
4
votes
0
replies
352
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
275
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
298
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
472
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
344
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
329
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
347
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
389
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
365
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
658
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
727
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 6 months ago by 76k • written 6 months ago by ▴ 40
1
vote
0
replies
462
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
726
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
9 weeks ago by Dr.Animo ▴ 60
2
votes
0
replies
847
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 ▴ 350
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 ▴ 350
4
votes
0
replies
947
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 ▴ 350
6
votes
0
replies
2.5k
views
Tutorial: How to download GEO data Quickly and easily
geo RNA-Seq R data-mining
6 months ago by Novogene ▴ 350
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 76k
1
vote
3
replies
688
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 6.0 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
How to assign read groups to bam files?
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
C: sra-explorer : find SRA and FastQ download URLs in a couple of clicks
Answer: Which function is best for pathway analysis?
Comment: Hisat2 index and alignment question
Answer: Low Alignment rate
Answer: Unable to build applet in DNAnexus, .jar file not found
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Popular Question to bharata1803 ▴ 550
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Recent Replies
Comment: Which function is best for pathway analysis? by luffy ▴ 40
@chris Please look into @Hamid Ghaedi's well documented [post][1] on ORA and GSEA, Or [this][2] documentation. Hope this helps. [1]: ht…
Comment: Bacterial Pangenome Analysis by kirankumareripogu ▴ 10
Hi @liorglic, Thank you for your prompt response. I totally agree with you that different blastp cuttoffs provide different results and…
Answer: Fetch Fastq files directly for SRA data by Rob 6.2k
What is the accession for the project? Many — though not all — of the projects present in the NCBI SRA are also hosted in the European Nuc…
Comment: Dataset's name in BioMart for S. pombe by YUYANG.OON • 0
Works with `useMart(biomart="fungi_mart", dataset="spombe_eg_gene", host="https://fungi.ensembl.org")`
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
This is still hard to interpret without the commands. What would help is if you literally copied the full UNIX commands along with their re…
Comment: Which function is best for pathway analysis? by Chris ▴ 180
Thank you for your reply! Do you have code that I and others can implement? I am not sure how to customize the gmt file from my differentia…
Comment: Bug of vg surject by Qi • 0
Thanks your reply! my resulte show below: 5x_pan_sv.bam 1347587601 #converted from gam to bam F1 indel=0.830392 snp=0.932511 5…
Comment: Bug of vg surject by Jordan M Eizenga ▴ 360
It might help us to diagnose the problem if you included the exact commands that you used and showed the results that you are concerned abo…
Answer: Which function is best for pathway analysis? by Yogi ▴ 20
Few things to mention. Pathway Enrichment Analysis can be split into two categories. 1. Functional Class Scoring Methods 2. Overrepr…
Answer: identify DEGs across all conditions and per specific conditions by Yogi ▴ 20
Couple of things. (Feel free to correct if I'm misunderstanding). "DESeq2" is meant for 1v1 comparisons. If you're trying to compar…
Comment: Hisat2 index and alignment question by Istvan Albert 98k
yes correct you have to pass the full prefix and not the directory
Comment: Low Alignment rate by dsull ★ 4.7k
Wow! Didn't realize the repeat-masked file could have such a large influence on alignment. Very good to know -- I guess I'll need to dive i…
Comment: Troubles launch IGV on Linux(Debian) by morovatunc ▴ 550
Disclaimer: My comment could be totally unrelated. I would give these a try if you have noone comment/answer your problem. I have had this…
Comment: How to check RNAseq support for annotated genes? by Michael 53k
> I tried it using STAR to map the transcript to the annotation gtf file That is not what STAR is for. STAR is for aligning short reads in…
Comment: Low Alignment rate by Mehwish • 0
Thanks alot! This worked out for me https://ftp.ensembl.org/pub/release-110/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna.toplevel.fa.gz …
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