Limit : all time
all time today this week this month this year
383 results • Page 1 of 8
Sort: Rank
Rank Views Votes Replies
0
votes
0
replies
170
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
5 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
242
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
443
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 4 weeks ago by 78k • written 7.7 years ago by 41k
1
vote
0
replies
268
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 11 weeks ago by 41k • written 11 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
366
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
316
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
501
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
422
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
436
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
646
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 28 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
658
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
517
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
437
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
629
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
467
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
518
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
518
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 7 months ago by 136k • written 10.0 years ago by 20k
2
votes
0
replies
854
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
591
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 23 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
A: How to add biological annotations using R
Answer: Mapping quality in `vg giraffe`
Answer: Mapping quality in `vg giraffe`
Answer: Comparing 3 Data Sets using DeSeq and Heatmaps
Comment: Harmony integration PC variance explained
Answer: Is bisulfite-seq data from different studies comparable with each other?
Answer: BULK mRNA-seq with UMIs. Do I need to normalize by gene length?
Recent Locations • All
Italy, just now
Basel, Switzerland, 1 minute ago
Malta, 3 minutes ago
Spain, 5 minutes ago
Bologna, 5 minutes ago
Belgium, 9 minutes ago
UCLA, 9 minutes ago
Recent Awards • All
Popular Question to massa.kassa.sc3na ▴ 590
Commentator to dsull ★ 5.0k
Scholar to Xian ▴ 60
Popular Question to sebabiokr ▴ 10
Popular Question to emmanouil.a ▴ 120
Popular Question to arshad1292 ▴ 100
Scholar to Philipp Bayer 8.1k
Recent Replies
Comment: Where is the index command? by Michael 53k
samtools index (like genral programs you install on your machine) should run without sudo, if it doesn't, you might want to check the acces…
Comment: Where is the index command? by Michael 53k
I didn't know you were using WSL. Possibly the damage you can do with that is limited to the WSL environment and the worst thing that can h…
Comment: Is bisulfite-seq data from different studies comparable with each other? by Basti ★ 1.8k
There is no general rule, what you can apply depends on the nature of each dataset you intend to integrate (tissue, condition, technique, s…
Comment: Where is the index command? by Michael 53k
Running this is always a good idea.
Answer: Salmon indices differences by ATpoint 78k
In theory the full genome decoy is the best since it includes the entire genome, hence decoying potential spurious mappings due to DNA cont…
Comment: Can you help me to download list of miRNA from a SRA under a bioproject ? by Nitin Narwade ★ 1.5k
You can directly ask authors but as it is still on bioRxiv I don't think they can share this data with you until it get published somewhere…
Comment: Can you help me to download list of miRNA from a SRA under a bioproject ? by abourrieau • 0
Thank you, I had thought about this possibility but I don't see where it is indicated on the NCBI website: : https://www.ncbi.nlm.nih.gov/b…
Comment: Cellcyclescoring did not work in Seurat V5 by fracarb8 ★ 1.3k
You can try to merge the layer together with `data.filt <- JoinLayers(data.filt)`
Comment: Mapping quality in `vg giraffe` by Wenhai • 0
Many thanks.
Comment: Can you help me to download list of miRNA from a SRA under a bioproject ? by Nitin Narwade ★ 1.5k
It seems the data for this BioProject is not publicly available yet. It is a good practice to check first on the NCBI website. Regards, N…
Comment: How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq) by Nitin Narwade ★ 1.5k
Hi, Nobody has answered you yet, probably because there are very basic things you assumed wrong, so I will try to comment on this. The f…
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge by KL_STKLBK • 0
This is not really answering the question - one can loop say VCFtools, but it would still be windows/single site based. DnaSP also does not…
Comment: Is bisulfite-seq data from different studies comparable with each other? by CTLong ▴ 20
Hi Colin, thanks for the reply. What about integration of RNA-seq expression from different studies? I guess this is more widely accepted r…
Comment: calculate nucleotide diversity from whole-genome-sequence data for individual ge by J • 0
Thanks, but I still need a method that actually calculates per gene nucleotide diversity. And as mentioned DnaSP6 does not give the option …
Comment: R script in docker by Jean-Karim Heriche 26k
This isn't a bioinformatics question. To access data that sits outside the container from within the container, you need to make it accessi…
Traffic: 1724 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6