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345 results • Page 2 of 7
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234
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176
replies
79k
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73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq TCGA Survival Tutorial
updated 4 weeks ago by 36k • written 7.0 years ago by ★ 4.6k
6
votes
0
replies
1.1k
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
16 months ago by rpolicastro 9.4k
8
votes
1
reply
793
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk fasta Tutorial
17 months ago by Kevin Blighe 82k
15
votes
9
replies
3.5k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R tidyverse gene Tutorial
updated 11 months ago by ★ 1.1k • written 23 months ago by 9.4k
12
votes
2
replies
859
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R Tutorial
16 months ago by rpolicastro 9.4k
147
votes
35
replies
56k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics Tutorial next-gen
updated 3 months ago by • 0 • written 9.7 years ago by ★ 1.6k
14
votes
2
replies
2.2k
views
Tutorial: Methylation Analysis Tutorial in R_part2
methylation RNA-Seq R cancer Tutorial
17 months ago by Hamid Ghaedi ★ 2.6k
4
votes
0
replies
1.4k
views
Tutorial: Building mosdepth on macOS
mosdepth nim Tutorial
16 months ago by ATpoint 64k
7
votes
6
replies
3.0k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
Software clusterProfiler Tool rna-seq tool
updated 11 months ago by 21k • written 17 months ago by ▴ 160
15
votes
7
replies
10.0k
views
Tutorial: Integrating VDJ sequencing data with Seurat
Seurat clonotyping VDJ sc-RNAseq Tutorial
updated 18 months ago by 8.4k • written 3.2 years ago by ▴ 300
270
votes
33
replies
84k
views
24 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 6 months ago by ▴ 100 • written 8.8 years ago by 20k
5
votes
0
replies
2.9k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap Tutorial
18 months ago by GenoMax 119k
10
votes
0
replies
3.3k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap Tutorial
18 months ago by GenoMax 119k
10
votes
0
replies
1.9k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap Tutorial
18 months ago by GenoMax 119k
11
votes
1
reply
1.8k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq Tutorial
updated 8 months ago by 64k • written 19 months ago by ★ 20k
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell Tutorial flow-cytometry
9 months ago by Ahill ★ 1.9k
0
votes
1
reply
2.1k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
taxonomy python biosql Tutorial
updated 20 months ago by • 0 • written 4.0 years ago by ▴ 310
76
votes
13
replies
14k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 10 months ago by 36k • written 8.2 years ago by 19k
6
votes
10
replies
3.9k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
dna methylation Tutorial DMR
20 months ago by dec986 ▴ 340
41
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
maf vcf ensembl tcga somatic Tutorial
20 months ago by Cyriac Kandoth 5.8k
5
votes
2
replies
3.9k
views
Tutorial: bam2rpkm by bedtools
RNA-Seq bam rpkm bedtools Tutorial
updated 20 months ago by 64k • written 4.8 years ago by ▴ 130
16
votes
11
replies
7.0k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation Tutorial
3 days ago by Ram 36k
41
votes
33
replies
6.2k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation Tutorial
20 months ago by Ram 36k
94
votes
6
replies
19k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
snakemake conda workflow Tutorial
updated 21 months ago by ▴ 50 • written 3.9 years ago by 15k
17
votes
40
replies
15k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
run easy orthomcl all-v-all mcl Tutorial
updated 21 months ago by ★ 1.9k • written 6.1 years ago by ▴ 160
23
votes
4
replies
5.4k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
enrichedheatmap chip-seq atac-seq heatmap Tutorial
updated 13 months ago by ★ 1.1k • written 3.0 years ago by 64k
13
votes
4
replies
3.8k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
R RNA-Seq Transcriptomics Tutorial bioconductor
6 months ago by Thind amarinder ▴ 270
26
votes
0
replies
1.8k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
variant interpretation annotation clinical cancer Tutorial
22 months ago by Malachi Griffith 19k
10
votes
1
reply
1.8k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
COVID-19 fastv Tutorial SARS-CoV-2
22 months ago by chen ★ 2.4k
60
votes
49
replies
37k
views
22 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 15 months ago by 36k • written 5.9 years ago by ★ 3.2k
10
votes
7
replies
3.6k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
STAR STARsolo 10x Chromium Tutorial
updated 7 months ago by 119k • written 23 months ago by 82k
15
votes
17
replies
5.6k
views
9 follow
Tutorial: Create de novo repeat library
Tutorial repeat annotation de-novo
updated 12 months ago by • 0 • written 2.7 years ago by ★ 7.2k
0
votes
0
replies
667
views
Tutorial: BrainArray CDF, annotation, etc
brainarray cdf db Tutorial
23 months ago by Kevin Blighe 82k
37
votes
0
replies
4.8k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
RNA-Seq batch correction edgeR ma-plot Tutorial
23 months ago by ATpoint 64k
10
votes
0
replies
1.7k
views
Tutorial: Long versus wide data for plotting genomics data in R.
R tidyverse ggplot2 Tutorial data.table
16 months ago by rpolicastro 9.4k
75
votes
70
replies
14k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment Tutorial david
updated 6 months ago by • 0 • written 4.5 years ago by 82k
1
vote
1
reply
877
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed txt bed2txt sequencing Tutorial
2.0 years ago by opheevallee • 0
4
votes
3
replies
3.6k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy tool R Tutorial
updated 14 months ago by ▴ 210 • written 4.4 years ago by ★ 3.9k
4
votes
1
reply
843
views
Tutorial: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED BEDtools Tutorial Video Lesson
2.0 years ago by sdsubaru33 ▴ 40
72
votes
59
replies
21k
views
15 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes PCA VCF PLINK Tutorial
updated 10 months ago by • 0 • written 4.9 years ago by 82k
3
votes
0
replies
2.1k
views
Tutorial: Sorting GFF/GTF files
annotation gff gtf sort Forum Tutorial
2.1 years ago by Juke34 ★ 7.2k
20
votes
6
replies
4.4k
views
Tutorial: Open Targets and programmatic access
drug API bioinformatics open targets disease Tutorial
2.1 years ago by Denise CS ★ 5.2k
2
votes
2
replies
1.2k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
SNP snpEff Annotation Tutorial chrMT
2.1 years ago by Arup Ghosh 3.0k
10
votes
3
replies
1.3k
views
Tutorial: FASTA file split
Tutorial split fasta tutorial
8 weeks ago by Juke34 ★ 7.2k
0
votes
0
replies
872
views
Tutorial: VIDEO: Installing BLAST Databases on Your Own Computer
sequence BLAST databases Linux MacOSX Tutorial
2.2 years ago by brian.fristensky ▴ 280
0
votes
0
replies
652
views
Tutorial: VIDEO: BLAST Searches Through a Data Science Lens
sequence BLAST Data Science Covid19 Tutorial
2.2 years ago by brian.fristensky ▴ 280
2
votes
1
reply
1.0k
views
Tutorial: A very simple way to detect viruses and microorganisms from mNGS FASTQ data using fastv
SARS-CoV-2 COVID-19 viruses fastv Tutorial
2.2 years ago by chen ★ 2.4k
65
votes
25
replies
22k
views
14 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
rna-seq tutorial Tutorial
updated 2.3 years ago by 36k • written 8.5 years ago by 94k
58
votes
41
replies
17k
views
16 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
arrow pbalign pacbio polishing smrt limk Tutorial
updated 2.3 years ago by • 0 • written 4.9 years ago by ★ 1.4k
20
votes
7
replies
5.2k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
RNA-Seq R ggplot2 Tutorial
2.3 years ago by ahmad mousavi ▴ 710
345 results • Page 2 of 7
Recent Votes
Why the result of GSEA and ssGSEA is different?
4-group RNAseq experiment- GSEA vs ssGSEA?
Are upset plots bad for differential expression analysis?
Answer: Are upset plots bad for differential expression analysis?
Answer: extracting sequences from a bam file
A: Best Genome Assembler and Genome Annotation tools and pipelines
Top/best RNAseq workflow including anlaysis results for function annotation
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Recent Replies
Answer: phylip format sequence name/header issue by Mensur Dlakic ★ 20k
Phylip format can have an arbitrary number of characters in header, but not all the programs will tolerate it. MrBayes, for example, has no…
Answer: phylip format sequence name/header issue by Michael Dondrup 52k
I assume you have the sequences in a FASTA file. I recommend to shorten the sequences in FASTA format already, then convert to phylip forma…
Comment: Extract sequences from a list of ID by Neel ▴ 20
Thank you....It has been done.
Comment: SNV, CNA, SV by Vincent Laufer ★ 2.2k
what exactly do you want to show about them. do you want to show the order in which they arose? or epistasis between them> ? or any other p…
Comment: Why weblogo of biopython doesn't work? by Plus • 0
Yes. I can try the web version of WebLogo, but I just want to know what kind of problem can induce to make a corrupted file by using Motif.…
Comment: Difference between clusterProfiler and gProfileR by Arup Ghosh 3.0k
> The GO terms output by gprofileR are generally quite similar to those > output by clusterProfiler, but there are small differences due to…
Comment: hgmd variants from Ensembl by Sanjar ▴ 140
Did you figure out how to do this?
Comment: Why weblogo of biopython doesn't work? by Arup Ghosh 3.0k
The `weblogo` module uses the web version of weblogo service and it seems the module is not working as intended. Instead of returning an im…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ by appropiate ▴ 40
Thanks @cmdcolin! It looks great, but being relatively new on the field and having started with IGV, I think I will stick to the latter and…
Comment: Extract sequences from a list of ID by GenoMax 119k
You need to remove `>` from ID's as the warning tells you to do.
Comment: The best way to get gene lengths for 15K+ genes? by manaswwm ▴ 260
From my previous experiences in retrieving data in bulk from biomaRt/Ensembl - it is always better to partition your data into batches befo…
Comment: Can IGV simultaneously show alignments for different reference genomes in differ by cmdcolin ★ 2.3k
disclaimer: I am a jbrowse 2 dev: you could consider jbrowse 2, which can load multiple genomes, visualize synteny, and look at the mapped …
Answer: download just a chromosome from SRA toolkit by ATpoint 64k
No, it is not possible since fastq are raw data without alignment information, hence without chromosomal information.
Answer: download just a chromosome from SRA toolkit by shelkmike ▴ 660
No, its impossible. Sequencing reads in SRA are not partitioned by chromosomes.
Comment: Extract sequences from a list of ID by Neel ▴ 20
Hi, i want to extract seq from list of id but Seqkit gives this below error and empty output file generated [WARN] symbol ">" detected…
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