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Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
4 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 23 days ago by ▴ 50 • written 3.3 years ago by ▴ 160
0
votes
0
replies
239
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
25 days ago by rohitsatyam102 ▴ 780
0
votes
4
replies
440
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
19 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 27 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 29 days ago by 78k • written 7.7 years ago by 41k
1
vote
0
replies
264
views
Tutorial: How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq heatmap rstats TCGA
4 weeks ago by Ming Tommy Tang ★ 3.6k
10
votes
31
replies
9.9k
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
363
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 10 weeks ago by 41k • written 10 weeks ago by 158k
0
votes
1
reply
314
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
421
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
365
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
685
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
315
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
355
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
3 months ago by barslmn ★ 2.0k
0
votes
0
replies
498
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
421
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
435
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
468
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
643
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 27 days 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
656
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
334
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
516
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
438
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
435
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
628
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
466
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
517
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
463
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
510
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
516
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
776
views
Tutorial: How to make a heatmap in R and deep understand it
heatmap r
6 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 6 months ago by 136k • written 10.0 years ago by 20k
2
votes
0
replies
853
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
590
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 22 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 19 months ago by ★ 3.3k
2
votes
0
replies
934
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
updated 16 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
How to make a survival plot for a gene between High expression and low expression samples?
Comment: bwa mem hangs after a few thousand reads
bwa mem hangs after a few thousand reads
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
Answer: Generate Read counts from bam file
Comment: Generate Read counts from bam file
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Recent Replies
Answer: Where is the index command? by Michael 53k
There is a ready-made package for samtools, simply do apt install samtools Also, your screenshot shows you are using the root account…
Comment: bwa mem hangs after a few thousand reads by tshtatland ▴ 170
Use option `-v` with value of 4 or above to help diagnose the issue: `-v INT` Control the verbose level of the output. This option has not…
Comment: bwa mem hangs after a few thousand reads by tshtatland ▴ 170
Cross-posted here: [sequence alignment - bwa mem hangs after a few thousand reads - Bioinformatics Stack Exchange](https://bioinformatics.s…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT by tw_140 • 0
Thank you, I really appreciate your insight! I will look into the dropouts I have.
Answer: Generate Read counts from bam file by NextGenSeek • 0
Are you analysing RNA or DNA heteroplasmy levels?
Comment: What type of cancer did they study in this paper? by GenoMax 136k
Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …
Comment: p-value combination methods by i.sudbery 18k
edgeR *is* an NB-GLM. The input to NB-GLMs, including edgeR and DESeq is read counts from each sample.
Answer: What type of cancer did they study in this paper? by jared.andrews07 ★ 16k
Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
Comment: p-value combination methods by sehriban.buyukkilic • 0
its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
Comment: How do I download a list of genes involved in cellular metabolism (in humans) ba by el24 ▴ 40
Hi @pratik, Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-spe…
Comment: Match variants for allele frequency, LD score, and other features by Jautis ▴ 520
Trying to bump this
Comment: p-value combination methods by i.sudbery 18k
The parameters you have here are the *output* of an NB-GLM, not the input to an NB-GLM (most likely edgeR?)
Comment: How can I adjust Y-axis scale when making relative abundance box plot ? by ATpoint 78k
Please provide data as dput(), not via any random dropbox, that could be anything (also malware, theoretically). If log transformation crea…
Comment: Extracting chimeric reads from mapping by doggie • 0
Hi Pierre, so does samjdk support single-end reads for extracting chimeric reads? I've aligned my virus to the human reference, sorted the …
Comment: How can I adjust Y-axis scale when making relative abundance box plot ? by dthorbur ▴ 870
You can try `scale_y_sqrt()` instead if you don't like the look of the log10 transformation. As an aside, it doesn't look like your fill va…
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