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379 results • Page 1 of 8
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Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 8 days ago by 40k • written 8 days ago by 157k
0
votes
1
reply
165
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 10 days ago by 76k • written 10 days ago by ▴ 30
4
votes
2
replies
2.3k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 17 days ago by 134k • written 3.4 years ago by 76k
0
votes
0
replies
217
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
29 days ago by Ming Tommy Tang ★ 3.4k
0
votes
0
replies
213
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
4 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
424
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
181
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
5 weeks ago by Ming Tommy Tang ★ 3.4k
9
votes
4
replies
3.9k
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
211
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
5 weeks ago by barslmn ★ 1.8k
0
votes
0
replies
218
views
Tutorial: How to preprocess and visualize beautifully scRNA-seq with omicverse?
scRNA-seq seurat scanpy Python
6 weeks ago by Starlitnightly • 0
1
vote
0
replies
279
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 7 weeks ago by 40k • written 7 weeks ago by ★ 3.4k
3
votes
1
reply
300
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 7 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 8 weeks ago by • 0 • written 7.5 years ago by 20k
1
vote
0
replies
301
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 9 weeks ago by 40k • written 9 weeks ago by ★ 3.4k
0
votes
0
replies
411
views
Tutorial: Differentially expressed gene analysis in Python with omicverse
RNA-seq Python
9 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 9 weeks ago by 76k • written 3.5 years ago by 5.5k
3
votes
2
replies
458
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
9 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 10 weeks ago by • 0 • written 5.2 years ago by ▴ 580
2
votes
0
replies
225
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 10 weeks ago by 40k • written 11 weeks ago by ★ 3.4k
4
votes
0
replies
345
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
12 weeks ago by Ming Tommy Tang ★ 3.4k
0
votes
0
replies
270
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 12 weeks ago by 40k • written 12 weeks ago by ★ 3.4k
0
votes
0
replies
288
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
12 weeks ago by sinha.shriprakash ▴ 20
1
vote
2
replies
462
views
Tutorial: How to ask computational biology questions
computational-biology
updated 12 weeks ago by 40k • written 12 weeks ago by ★ 3.4k
1
vote
0
replies
334
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
318
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
339
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
381
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
358
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
649
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 9.8 years ago by 20k
2
votes
0
replies
720
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
458
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
721
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
5 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
1.5k
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
838
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 8 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 8 months ago by ▴ 350
4
votes
0
replies
939
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 8 months ago by ▴ 350
6
votes
0
replies
2.4k
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
682
views
Tutorial: Gibbs Sampling Algorithm Implementation for Searching DNA Motifs
montecarlo DNA motif gibbssampling splice
5 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
Answer: Chromosome bias on RNA-Seq differential gene expression analysis
Answer: Simulate short-read RNA-seq data from long-read RNA-seq data
Comment: Chromosome bias on RNA-Seq differential gene expression analysis
Convert Human to Mouse Symbols
Convert Human to Mouse Symbols
Answer: Convert Human to Mouse Symbols
Comment: kallisto normalized TPM values without bootstraps
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Recent Replies
Comment: Dealing with transcriptome sequences that are smaller than their respective gene by langziv ▴ 50
I have aligned the RNA to the strain's genome from NCBI. The issue is that some RNA sequences that match CDSs from the genome, match them p…
Answer: How to find out what adapters to remove after FastQC of RNAseq data? by GenoMax 134k
You can use bbduk.sh from BBMap suite (https://www.biostars.org/p/175003/#175005 ) or `fastp` to figure out what potential adapter sequence…
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Thanks for pointing out. Let me explain: I had VCF files with gnomad 2.1.1 variants (chromosome positions). I performed a liftover with Pi…
Comment: STAR Intron Motif Script Gives Segmentation fault Error by Y • 0
I still get the error: line 65: 29089 Segmentation fault I am not sure why this is occurring.
Comment: Dealing with transcriptome sequences that are smaller than their respective gene by GenoMax 134k
Align your data to one of the genomes available at NCBI. There is no way your strain is completely different than the common reference. If …
Comment: Chromosome bias on RNA-Seq differential gene expression analysis by blz ▴ 20
I highlighted all the genes from that chromosome in the volcano plot and, as you can see below, many genes are below threshold of p-value a…
Comment: Chipseq analysis on repeat genes by pb11 ▴ 10
I tried that method and I am unable to capture that. I see in my RNAseq that repeat elements are enriched and we I see the chipseq marks ov…
Comment: Chromosome bias on RNA-Seq differential gene expression analysis by blz ▴ 20
It could be possible to observe an extra copy only in the knockout, it's a (pathogenic) plastic microorganism. But it's unlikely to happen …
Comment: Trimmomatic .jar not included anymore? by Pierre Lindenbaum 157k
please review all your previous questions and validate the correct answers (green tick on the left): https://www.biostars.org/p/9575583 htt…
Answer: Trimmomatic .jar not included anymore? by Pierre Lindenbaum 157k
> The command I used to run trimmomatic is this java -jar /storage/home/sjw6257/tools/Trimmomatic-0.39/ java -jar argument should be a f…
Comment: Trimmomatic .jar not included anymore? by petebio ▴ 80
I am guessing that you actually downloaded the source files and not the compiled binary which is why you are missing the .jar file? If this…
Answer: Highly inflated p-values in GWAS by regenie by SushiRoll ▴ 110
Hi! Just jumping in with a suggestion rather than an answer, could it be that the p-values you're getting are not adjusted for multiple com…
Comment: kallisto normalized TPM values without bootstraps by butterman16 ▴ 20
Thank you! Not really sure why I assumed the values had to come from sleuth, but tximport/DESeq2 worked great!
Comment: Weirdness in annotation (missing allele frequencies) by Jeremy Leipzig 21k
before we dive in too deep let's confirm we are on the same page that gnomad 2.1.1 (in your text) is in hg37. gnomad 3.1.2 (in your screens…
Comment: Finding sequences in unannotated genomes using reference coordinates by Pierre Lindenbaum 157k
related: https://www.biostars.org/p/49627
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