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Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
7 days ago by rohitsatyam102 ▴ 780
36
votes
14
replies
32k
views
14 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 25 days ago by ▴ 50 • written 3.3 years ago by ▴ 160
0
votes
0
replies
247
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
27 days ago by rohitsatyam102 ▴ 780
0
votes
4
replies
452
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
21 days ago by Coremine Medical ▴ 20
90
votes
48
replies
31k
views
29 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 29 days ago by 41k • written 10.1 years ago by ★ 7.8k
48
votes
30
replies
9.3k
views
11 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 4 weeks ago by 78k • written 7.7 years ago by 41k
1
vote
0
replies
274
views
Tutorial: How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq heatmap rstats TCGA
5 weeks ago by Ming Tommy Tang ★ 3.6k
10
votes
31
replies
10.0k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 5 weeks ago by • 0 • written 5.9 years ago by ▴ 320
2
votes
0
replies
366
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 11 weeks ago by 41k • written 11 weeks ago by 158k
0
votes
1
reply
319
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 11 weeks ago by 78k • written 11 weeks ago by ▴ 30
4
votes
2
replies
2.5k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 12 weeks ago by 136k • written 3.6 years ago by 78k
0
votes
0
replies
424
views
Tutorial: multi-omics data integration: a case study with transcriptomics and genomics mutation data
mutation RNAseq multiomics
3 months ago by Ming Tommy Tang ★ 3.6k
0
votes
0
replies
368
views
Tutorial: T Cell Clonal Analysis Using Single-cell RNA Sequencing and Reference Maps
RNAseq TCR single-cell computational biology
3 months ago by Ming Tommy Tang ★ 3.6k
13
votes
3
replies
14k
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 3 months ago by ▴ 20 • written 6.7 years ago by ★ 1.6k
5
votes
2
replies
696
views
Tutorial: Updated List of Unix tutorials 2023
Unix
updated 3 months ago by 41k • written 3 months ago by ★ 2.4k
0
votes
0
replies
319
views
Tutorial: cellular niches analysis with spatial transcriptome data in Seurat and Bioconductor
transcriptome rstats spatial single-cell
3 months ago by Ming Tommy Tang ★ 3.6k
9
votes
4
replies
4.5k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
3 months ago by Hamid Ghaedi 3.1k
6
votes
0
replies
359
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
3 months ago by barslmn ★ 2.0k
0
votes
0
replies
506
views
Tutorial: How to preprocess and visualize beautifully scRNA-seq with omicverse?
scRNA-seq seurat scanpy Python
3 months ago by Starlitnightly • 0
1
vote
0
replies
424
views
Tutorial: common mistakes in using spreadsheets
excel spreadsheet structured-data
updated 4 months ago by 41k • written 4 months ago by ★ 3.6k
3
votes
1
reply
438
views
Tutorial: Coordinate Systems and genomic variant description
coordinate-system HGVS normalization VCF
updated 4 months ago by 41k • written 4 months ago by 8.4k
84
votes
29
replies
30k
views
20 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 4 months ago by • 0 • written 7.7 years ago by 20k
1
vote
0
replies
470
views
Tutorial: How to convert gene ids in R
computational-biology gene-id rstats
updated 4 months ago by 41k • written 4 months ago by ★ 3.6k
0
votes
0
replies
654
views
Tutorial: Differentially expressed gene analysis in Python with omicverse
RNA-seq Python
4 months ago by Starlitnightly • 0
19
votes
13
replies
7.9k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 4 weeks ago by • 0 • written 17 months ago by 78k
2
votes
0
replies
2.9k
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 4 months ago by 41k • written 4 months ago by ★ 3.6k
18
votes
7
replies
6.0k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 4 months ago by 78k • written 3.7 years ago by 5.7k
3
votes
2
replies
663
views
Tutorial: How to use UCSC genome browser to check the transcription factor binding at your favorite gene
UCSC transcription factor ChIP-seq
4 months ago by Ming Tommy Tang ★ 3.6k
88
votes
22
replies
83k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 4 months ago by • 0 • written 5.4 years ago by ▴ 580
2
votes
0
replies
335
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 4 months ago by 41k • written 4 months ago by ★ 3.6k
4
votes
0
replies
520
views
Tutorial: How to do GSEA in R for RNAseq data
gsea RNAseq rstats
5 months ago by Ming Tommy Tang ★ 3.6k
0
votes
0
replies
442
views
Tutorial: How to read all files into a single dataframe (merge all RNAseq count table)
RNA-seq rstats
updated 5 months ago by 41k • written 5 months ago by ★ 3.6k
0
votes
0
replies
440
views
Tutorial: Free Book : Computational Biology of a cell signalling pathway using R
cell-signalling R Computational-Biology
5 months ago by sinha.shriprakash ▴ 20
1
vote
2
replies
631
views
Tutorial: How to ask computational biology questions
computational-biology
updated 5 months ago by 41k • written 5 months ago by ★ 3.6k
1
vote
0
replies
470
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 5 months ago by 41k • written 5 months ago by ★ 3.6k
2
votes
0
replies
520
views
Tutorial: best practices for single-cell RNAseq analysis
cell single scRNAseq
5 months ago by Ming Tommy Tang ★ 3.6k
1
vote
0
replies
466
views
Tutorial: How to make a perfect heatmap using RNAseq data
heatmap RNAseq rstats
5 months ago by Ming Tommy Tang ★ 3.6k
0
votes
0
replies
513
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
5 months ago by Coremine Medical ▴ 20
2
votes
0
replies
521
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 5 months ago by 41k • written 5 months ago by ▴ 20
3
votes
0
replies
778
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
7 months ago by Ming Tommy Tang ★ 3.6k
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 7 months ago by 136k • written 10.0 years ago by 20k
2
votes
0
replies
858
views
Tutorial: ChIP-Seq Analysis Tutorial
Epigenetics Bowtie2 MACS2 ChIP-Seq Motif
updated 8 months ago by 78k • written 8 months ago by ▴ 40
1
vote
0
replies
593
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 25 days ago by 41k • written 8 months ago by ▴ 10
3
votes
2
replies
2.5k
views
Tutorial: Continuing Education (Pipelines): Best blogs, Online Lectures, Workshops, etc..
conferences Workshops
updated 6 months ago by 41k • written 6.6 years ago by ▴ 100
7
votes
3
replies
2.0k
views
Tutorial: Automated dbSNP lookup by rsID position, plus genome build liftover
rsid hg19 liftover hg38 dbsnp
updated 7 months ago by ▴ 110 • written 15 months ago by 86k
3
votes
3
replies
2.4k
views
Tutorial: Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC TCGABiolinks STAR
updated 9 months ago by 41k • written 20 months ago by ★ 3.3k
2
votes
0
replies
941
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
updated 18 days ago by • 0 • written 10 months ago by ★ 1.6k
11
votes
7
replies
1.9k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
8 months ago by barslmn ★ 2.0k
2
votes
1
reply
1.9k
views
Tutorial: Converting TSV file to VCF
vcf preprocessing frequency
updated 10 months ago by 158k • written 10 months ago by ★ 2.0k
4
votes
2
replies
1.9k
views
Tutorial: Prediction of Ribosomal RNA Genes Using RNAmmer Software
Annotation rRNA RNAmmer Genome
4 months ago by Dr.Animo ▴ 80
383 results • Page 1 of 8
Recent Votes
Comment: Problematic fastq files...How can we trust them?
Comment: Problematic fastq files...How can we trust them?
Answer: GO categorization
Comment: Using metagenome assembly and binning to identify and mitigate contamination in
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
Answer: How to obtain data on the coordinates of the Exon region from UCSC
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Scholar to ATpoint 78k
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Recent Replies
Comment: Bioinformatics by ATpoint 78k
Converting data from one to another format and repairing gene names turned dates. Yes, great field.
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with by GenoMax 136k
Yes that should be true. I will let https://www.biostars.org/u/14684/ confirm.
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks for the answe and the linkI used bioinfokit tpm formula to calculate tpm from bulk which is the same formula given in your link: A= …
Comment: From TPM to raw counts by Gama313 ▴ 120
Thanks Brian for the suggestion. However, I did the whole process, from bulk counts generation, to data transformation and scrna deconvolut…
Answer: Are 10x cellranger-arc ATAC bam files deduplicated? by swbarnes2 13k
My experience with regular 10x bam files is that duplicates are not removed, but they are flagged as duplicates. So take a look at the …
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by fluke • 0
Thanks a lot for your answer, I’m confused between RSEM expected count and RSEM normalized count. I’m working on this dataset from UCSC ht…
Answer: From TPM to raw counts by Istvan Albert 99k
In principle, the TPM formula can be reverted, see the timeless post * [What the FPKM? A review of RNA-Seq expression units][1] In p…
Comment: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by beausoleilmo ▴ 560
You're right, I wasn't explaining the problem clearly. Thanks for the directions! - The depth; coverage ~3.00X ± 2.50 SD - The sequen…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
All good points, especially about multiple copies of single-copy genes. I am doing error-correction in my assemblies, but was making an edu…
Comment: Can I use TCGA-LUAD RNAseq count that had already normalized by RSEM in Limma-vo by CTLong ▴ 20
Yes, normalized RSEM counts from TCGA can be used as input for Limma Voom. Please check this post https://support.bioconductor.org/p/63981/…
Comment: How to obtain data on the coordinates of the Exon region from UCSC by ayasu • 0
Sorry for the delay in expressing my thanks. I found the advice to look at the information from MySQL very useful. I will also refer to t…
Comment: From TPM to raw counts by Brian Bushnell 19k
I'm posting this as a comment instead of an answer specifically because it's just what I would do and I don't know if it's the best approac…
Comment: Using metagenome assembly and binning to identify and mitigate contamination in by Brian Bushnell 19k
In most cases error-correction should take care of error-spawned fake minor alleles, though... > If you want to convince yourself of this,…
Answer: Using metagenome assembly and binning to identify and mitigate contamination in by Mensur Dlakic ★ 25k
It is a valid question, and I particularly like when posters err on the side of providing more than less detail. Metagenomic binning can be…
Answer: Low coverage whole genome sequencing reveal excess heterozygosity for multiple S by Brian Bushnell 19k
I don't understand your plot. Perhaps a legend would help? I also don't know what you mean by "genotype frequency"; is that the ratio of …
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