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Tutorial: download metadata using GEOquery
biology GEO metadata computational
1 day ago by Ming Tommy Tang ★ 3.6k
1
vote
0
replies
128
views
Tutorial: CITEseq tutorial
CITEseq Alevin Seurat
4 days ago by Ming Tommy Tang ★ 3.6k
0
votes
0
replies
192
views
Tutorial: Making Tile plots to show Synonymous Non-Synonymous mutation fraction
mutation ggplotify geom_tile ggplot2
16 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 4 weeks ago by ▴ 50 • written 3.3 years ago by ▴ 160
0
votes
0
replies
271
views
Tutorial: Using easyPubMed and scholar package to get all citations of your paper
scholar easyPubMed
5 weeks ago by rohitsatyam102 ▴ 780
0
votes
4
replies
471
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
4 weeks 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 5 weeks ago by 41k • written 10.2 years ago by ★ 7.8k
48
votes
30
replies
9.4k
views
11 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 5 weeks ago by 78k • written 7.8 years ago by 41k
1
vote
0
replies
307
views
Tutorial: How to convert raw counts to TPM for TCGA data and make a heatmap across cancer types
RNAseq heatmap rstats TCGA
6 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 6 weeks ago by • 0 • written 5.9 years ago by ▴ 320
2
votes
0
replies
380
views
Tutorial: Managing your data (BAM, VCF, sample, phenotype) with RDF and SPARQL.
rdf sparql data-management graph
updated 12 weeks ago by 41k • written 12 weeks ago by 158k
0
votes
1
reply
345
views
Tutorial: TAPIS installation and usage
APA Iso-seq splicing TAPIS analysis alternative
updated 12 weeks ago by 78k • written 3 months ago by ▴ 30
4
votes
2
replies
2.5k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 3 months ago by 136k • written 3.6 years ago by 78k
0
votes
0
replies
445
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
388
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
733
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
340
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
4.6k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
4 months ago by Hamid Ghaedi 3.1k
6
votes
0
replies
373
views
Tutorial: Polygenic Risk Score Calculation
genetic-burden r prs ggplot glm
3 months ago by barslmn ★ 2.0k
0
votes
0
replies
542
views
Tutorial: How to preprocess and visualize beautifully scRNA-seq with omicverse?
scRNA-seq seurat scanpy Python
4 months ago by Starlitnightly • 0
1
vote
0
replies
438
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
456
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 7.8 years ago by 20k
1
vote
0
replies
481
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
682
views
Tutorial: Differentially expressed gene analysis in Python with omicverse
RNA-seq Python
4 months ago by Starlitnightly • 0
19
votes
13
replies
8.1k
views
10 follow
Tutorial: Setting up Aspera Connect (ascp) on Linux and macOS
ascp aspera
updated 5 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 5 months ago by 41k • written 5 months ago by ★ 3.6k
19
votes
7
replies
6.1k
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 5.8k
3
votes
2
replies
684
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
84k
views
14 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 5 months ago by • 0 • written 5.4 years ago by ▴ 580
2
votes
0
replies
347
views
Tutorial: Understanding Hierarchical Clustering in R, Distance Measures, and Linkage Methods
clustering gene-expression rstats
updated 5 months ago by 41k • written 5 months ago by ★ 3.6k
4
votes
0
replies
553
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
456
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
466
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
647
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
492
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
532
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
480
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
529
views
Tutorial: How to start disease research quickly and easily?
proteins pathways disease research-design genes
6 months ago by Coremine Medical ▴ 20
2
votes
0
replies
533
views
Tutorial: Get a list of genes associated with a drug in 1 min
drug genes drug-targets
updated 6 months ago by 41k • written 6 months ago by ▴ 20
3
votes
0
replies
792
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 10.1 years ago by 20k
2
votes
0
replies
875
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
616
views
Tutorial: List of Machine Learning-Based Scoring Function Papers
machine-learning docking papers
updated 4 weeks 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 7 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 8 months ago by ▴ 110 • written 16 months ago by 86k
3
votes
3
replies
2.5k
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
966
views
Tutorial: Analysis of Smart-Seq3 data with kallisto-bustools
single-cell kallisto transcriptomics smart-seq3 pipeline
updated 27 days ago by • 0 • written 10 months ago by ★ 1.6k
11
votes
7
replies
2.0k
views
Tutorial: Sequence Alignment from Scratch with BWA
alignment bwa DNA
8 months ago by barslmn ★ 2.0k
385 results • Page 1 of 8
Recent Votes
Answer: How to speed-up to contruct phylogenetic tree
Comment: How to speed-up to contruct phylogenetic tree
Answer: Renaming fasta files with their headers
Comment: What apps can read large FASTQ files on Windows?
Answer: Renaming fasta files with their headers
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
Answer: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 202
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Recent Replies
Answer: How to speed-up to contruct phylogenetic tree by Michael 53k
I agree with the other recommendations and I wouldn't recommend MEGA either, but would like to add that most programs, including MEGA, have…
Comment: Renaming fasta files with their headers by sebabiokr ▴ 10
Yes, Its perfectly working.. It will be useful if you share concat command too if there are same genes in the fasta file Thank you
Answer: Renaming fasta files with their headers by shenwei356 8.3k
I've got a general method, but you need to have some basic knowledge of regular expressions. If not, please learn them for 30 minutes: -…
Comment: Renaming fasta files with their headers by liorglic ★ 1.3k
It's hard to understand what your input and desired output look like. Please edit your original question so it includes a clear explanation…
Comment: SRA toolkit (NCBI) - sra to fasta by ATpoint 78k
Can be 23 or 109, it does not matter.
Comment: Renaming fasta files with their headers by sebabiokr ▴ 10
Thank you for your code, but i have a fasta file which contains [gene=rps12] ids, so i want to rename the header with gene id alone like >r…
Answer: How to speed-up to contruct phylogenetic tree by Mensur Dlakic ★ 25k
It depends on how long your protein is. Generally speaking, it shouldn't take weeks or months. Trees with more than ~100 branches are very …
Comment: How to speed-up to contruct phylogenetic tree by liorglic ★ 1.3k
Is there a specific reason you need to use MEGA? Maybe try another software which might be faster (e.g. PhyML, RaxML, IQ-TREE). Also, do yo…
Answer: Renaming fasta files with their headers by liorglic ★ 1.3k
Assuming that you have a directory containing multiple files with `.fasta` extension, each containing one record, you can do something like…
Comment: What are the methods to correlate/study metabolomics data to proteomics data? by LauferVA 3.8k
thank you, @wuschel, for the comprehensive reply.
Comment: Renaming fasta files with their headers by sebabiokr ▴ 10
i tried this command awk -F 'gene=|]|[.]{1}' '/^>/ {print $2}' 7seqNC_018552.1cds.fasta > 7NC_018552.fasta got only gene name alone wit…
Answer: Converting a .frq file to a data frame? by zau saa ▴ 70
simply add a word to line 1 as the name of column 6
Comment: SRA toolkit (NCBI) - sra to fasta by Sanjukta • 0
Hi there, will it be an issue if we do not mention 60?
Comment: Renaming fasta files with their headers by sebabiokr ▴ 10
Yes there are many answer in this forum but they are specific to header line. it doesnot work with my header line and its difficult for me …
Answer: What are the methods to correlate/study metabolomics data to proteomics data? by WUSCHEL ▴ 740
There are various methods to correlate and study metabolomics data to proteomics data. These methods can be broadly categorized into: 1. C…
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