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Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 20 days ago by 40k • written 20 days ago by 157k
0
votes
1
reply
193
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 22 days ago by 77k • written 22 days ago by ▴ 30
4
votes
2
replies
2.3k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 29 days ago by 135k • written 3.4 years ago by 77k
0
votes
0
replies
249
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
237
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
6 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
465
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 7 weeks ago by 40k • written 7 weeks ago by ★ 2.4k
0
votes
0
replies
195
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
7 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
223
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
7 weeks ago by barslmn ★ 1.9k
0
votes
0
replies
248
views
Tutorial: How to preprocess and visualize beautifully scRNA-seq with omicverse?
scRNA-seq seurat scanpy Python
8 weeks ago by Starlitnightly • 0
1
vote
0
replies
305
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 9 weeks ago by 40k • written 9 weeks ago by ★ 3.4k
3
votes
1
reply
320
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 9 weeks ago by 40k • written 9 weeks ago by 8.3k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 10 weeks ago by • 0 • written 7.6 years ago by 20k
1
vote
0
replies
324
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 11 weeks ago by 40k • written 11 weeks ago by ★ 3.4k
0
votes
0
replies
448
views
Tutorial: Differentially expressed gene analysis in Python with omicverse
RNA-seq Python
11 weeks ago by Starlitnightly • 0
19
votes
13
replies
6.9k
views
9 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 5 days 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 11 weeks ago by 77k • written 3.5 years ago by 5.5k
3
votes
2
replies
474
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
11 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 12 weeks ago by • 0 • written 5.2 years ago by ▴ 580
2
votes
0
replies
240
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 12 weeks ago by 40k • written 3 months ago by ★ 3.4k
4
votes
0
replies
363
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
287
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
310
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
489
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
354
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
346
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
359
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
394
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
4 months ago by Coremine Medical ▴ 10
1
vote
0
replies
369
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 4 months ago by 40k • written 4 months ago by ▴ 10
3
votes
0
replies
665
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
5 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 5 months ago by 135k • written 9.9 years ago by 20k
2
votes
0
replies
737
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
474
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 18 months ago by ★ 3.3k
1
vote
0
replies
739
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 ★ 1.9k
2
votes
1
reply
1.6k
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 8 months ago by 157k • written 8 months ago by ★ 1.9k
4
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 ▴ 70
2
votes
0
replies
857
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
976
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 3.1 years ago by 77k
1
vote
3
replies
700
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
6 months ago by barslmn ★ 1.9k
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
14
votes
31
replies
5.8k
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 8.3k
379 results • Page 1 of 8
Recent Votes
Comment: STAR Genome index Error
Answer: counting from a single BAM file with multiple samples
In Silico Genome Digestion ?
Genomic Restriction Finder
Comment: How do you validate and verify your pipeline's software updates?
Comment: How do you validate and verify your pipeline's software updates?
Issues with Mixture file when using CIBERSORTx
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Recent Replies
Comment: STAR Genome index Error by Ram 40k
Why did you add it in the middle instead of at the end? Run this: ``` STAR --runMode genomeGenerate \ --genomeDir GRCh38.79.chrom1 \ --gen…
Comment: STAR Genome index Error by Prasanna • 0
Thank you very much
Comment: What is the blue and red exactly in Plotheatmap after computeMatrix of my chip-s by Ram 40k
> I'm using Galaxy You should ask https://help.galaxyproject.org/
Comment: "MethylKit" package for WGBS data by Ram 40k
Why is this added as an **answer** to a 2 year old question?
Comment: STAR Genome index Error by Ram 40k
Ask the system administrator. From your prompt, it looks like you're on a login node. DO NOT RUN high memory/long-running jobs on a login n…
Comment: STAR Genome index Error by Ram 40k
What does that even mean? What is an "online cluster"?
Comment: How do you validate and verify your pipeline's software updates? by Ram 40k
> 15-50 bugs in every 1000 lines of code That's surprisingly low. Attention to software dev best practices will definitely help, so will …
Comment: How to check RNAseq support for annotated genes? by Michael 53k
I am not sure you can restrict the regions of alignment in STAR. The GTF file is to provide information on splice sites and possibly read c…
Comment: How do you validate and verify your pipeline's software updates? by kieran • 0
Do you think more attention to software best practices from a software engineering standpoint would be beneficial from a cost to benefit st…
Answer: counting from a single BAM file with multiple samples by dr-device ▴ 10
I ended up splitting the BAM file by cell barcode using my own custom script and then using featureCounts individually on each BAM file bef…
Comment: Split a concatenated alignment in multiple files by Felipe • 0
Hi, your code seem to be working in my case, but its deleting the last individual from my original alignment. It has a total of 60 individu…
Comment: STAR Genome index Error by GenoMax 135k
Code itself looks fine. If you are trying to run this on a cluster without going through the job scheduler then it is possible that admins …
Answer: "MethylKit" package for WGBS data by viveksomya123 • 0
I ran the `annotateWithGeneParts()` function in methylkit but I am getting below error. Kindly help. List of command is as follow ```r li…
Comment: STAR Genome index Error by Prasanna • 0
Can you please suggest how can I modify the code ... Thanks!
Comment: STAR Genome index Error by Prasanna • 0
Thanks There is no error
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