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224
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Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq TCGA Survival Tutorial
updated 16 days ago by 32k • written 5.7 years ago by ★ 4.3k
110
votes
115
replies
14k
views
18 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
updated 9 months ago by ▴ 10 • written 2.5 years ago by 72k
67
votes
68
replies
10k
views
16 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment Tutorial david
updated 10 days ago by ▴ 900 • written 3.1 years ago by 72k
129
votes
66
replies
29k
views
15 follow
Tutorial: Network plot from expression data in R using igraph
R Tutorial microarray RNA-Seq network
14 months ago by Kevin Blighe 72k
104
votes
66
replies
24k
views
20 follow
Tutorial: Fast download of FASTQ files from the European Nucleotide Archive (ENA)
ENA Fastq fastq-dump aspera Tutorial
updated 7 months ago by ▴ 30 • written 2.8 years ago by 47k
65
votes
61
replies
15k
views
14 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000 genomes PLINK PCA Tutorial
8 months ago by Kevin Blighe 72k
70
votes
56
replies
16k
views
13 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes PCA VCF PLINK Tutorial
8 months ago by Kevin Blighe 72k
72
votes
48
replies
13k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
bwa alignment ngs tutorial Tutorial
updated 8.0 years ago by ▴ 10 • written 8.2 years ago by 32k
54
votes
47
replies
32k
views
20 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 6 months ago by • 0 • written 4.5 years ago by ★ 2.9k
180
votes
46
replies
62k
views
30 follow
Tutorial: Analysing Microarray Data In Bioconductor
tutorial bioconductor microarray analysis tutorial Tutorial
updated 11 months ago by • 0 • written 8.5 years ago by 19k
51
votes
41
replies
14k
views
16 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
arrow pbalign pacbio polishing smrt limk Tutorial
updated 11 months ago by • 0 • written 3.6 years ago by ★ 1.3k
15
votes
40
replies
12k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
run easy orthomcl all-v-all mcl Tutorial
updated 5 months ago by ★ 1.8k • written 4.8 years ago by ▴ 140
66
votes
39
replies
21k
views
20 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
rna-seq bioconductor fpkm Forum Tutorial
updated 5 months ago by 32k • written 7.5 years ago by ★ 7.3k
250
votes
38
replies
124k
views
25 follow
Tutorial: How to download raw sequence data from GEO/SRA
GEO SRA fastq bam download Tutorial
updated 15 months ago by ▴ 60 • written 6.6 years ago by 19k
143
votes
34
replies
49k
views
31 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen tutorial Tutorial
updated 25 days ago by ▴ 90 • written 8.4 years ago by ★ 1.6k
40
votes
33
replies
4.8k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation Tutorial
4 months ago by Ram 32k
67
votes
32
replies
9.6k
views
17 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
R pathway enrichment active subnetwork Tutorial
updated 6 weeks ago by • 0 • written 2.8 years ago by ★ 1.1k
228
votes
32
replies
67k
views
22 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 7 weeks ago by ▴ 10 • written 7.5 years ago by 19k
137
votes
32
replies
44k
views
15 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
mutation maf tcga cancer music Tutorial
updated 3.1 years ago by ★ 8.6k • written 8.0 years ago by 5.5k
79
votes
26
replies
21k
views
15 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
GenVisR BioConductor R Graphics Tutorial
updated 2.7 years ago by ▴ 10 • written 5.1 years ago by 19k
58
votes
26
replies
7.6k
views
7 follow
Tutorial: Parallel processing in R
R Tutorial biocparallel mclapply foreach
17 months ago by Kevin Blighe 72k
57
votes
25
replies
29k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC TCGA Download methylation Tutorial
updated 2.4 years ago by 47k • written 4.7 years ago by ★ 8.6k
62
votes
25
replies
19k
views
12 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
rna-seq tutorial Tutorial
updated 11 months ago by 32k • written 7.2 years ago by 87k
119
votes
25
replies
60k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
samtools bedtools bwa unix Tutorial
updated 5.4 years ago by ▴ 30 • written 9.0 years ago by ★ 4.0k
94
votes
25
replies
29k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality fastq trimming qc tutorial Tutorial
updated 6.3 years ago by ▴ 10 • written 8.5 years ago by 87k
7
votes
23
replies
6.2k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
orthomcl ubuntu linux mysql Tutorial
2.9 years ago by Vimal Kumar Velayudhan ▴ 200
140
votes
21
replies
26k
views
12 follow
Tutorial: A few words for R beginners
Swirl R beginner Tutorial
updated 4.6 years ago by ▴ 30 • written 6.3 years ago by ★ 1.5k
8
votes
19
replies
11k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
orthomcl mysql no root local Tutorial
updated 5.3 years ago by ▴ 670 • written 6.4 years ago by ▴ 560
49
votes
19
replies
37k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
chip-seq rna-seq bigwig visualization ucsc tutorial Tutorial
updated 5.2 years ago by ★ 8.6k • written 9.0 years ago by 10k
84
votes
19
replies
27k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
classification microarray expression bioconductor Tutorial
updated 4.3 years ago by • 0 • written 7.4 years ago by 19k
47
votes
19
replies
10k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
fastqc qualitycontrol tutorial Tutorial
updated 8.1 years ago by ▴ 140 • written 8.1 years ago by 87k
42
votes
19
replies
6.2k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software tutorial Tutorial
8.1 years ago by Daniel Standage 4.0k
23
votes
19
replies
4.2k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
mutation fastq cancer target Tutorial
updated 3.2 years ago by • 0 • written 4.5 years ago by ★ 2.1k
11
votes
18
replies
5.7k
views
8 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat single cell RNA-Seq TCR Tutorial
updated 22 months ago by ▴ 260 • written 22 months ago by 9.1k
10
votes
17
replies
1.6k
views
Tutorial: gene set filter/selection for training ab initio annotation tools
genome gene Tutorial
12 months ago by Juke34 ★ 5.3k
26
votes
17
replies
5.5k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv Tutorial
updated 5.6 years ago by ▴ 10 • written 6.7 years ago by 5.7k
8
votes
17
replies
1.7k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
Tutorials RNA-seq alignment next-gen sequencing
5.5 years ago by elia.brodsky ▴ 340
12
votes
17
replies
1.7k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa Tutorial
5.8 years ago by Istvan Albert 87k
40
votes
16
replies
17k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
CNV varscan2 GISTIC copy-number Tutorial
written 5.6 years ago by ★ 2.3k
13
votes
16
replies
2.6k
views
7 follow
Tutorial: Create de novo repeat library
annotation repeat de-novo Tutorial
6 months ago by Juke34 ★ 5.3k
30
votes
16
replies
13k
views
10 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
classification tutorial Tutorial
4.0 years ago by Obi Griffith 19k
52
votes
15
replies
38k
views
8 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools bcftools htslib Tutorial
2.7 years ago by otwtgin2010 ▴ 340
83
votes
15
replies
22k
views
16 follow
Tutorial: Heatmaps in R
heatmap R Tutorial
7 months ago by Jean-Karim Heriche 24k
33
votes
15
replies
14k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
R TCGA GDC next-gen Tutorial
updated 2.1 years ago by ▴ 30 • written 4.5 years ago by ▴ 300
22
votes
15
replies
6.5k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
bioinformatics training tutorial Tutorial
3.8 years ago by Medhat 8.9k
19
votes
15
replies
2.2k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf Tutorial
17 months ago by Shicheng Guo ★ 8.6k
50
votes
15
replies
6.7k
views
Tutorial: Which human reference genome should I use?
genome alignment assembly Tutorial
2.4 years ago by finswimmer 14k
20
votes
14
replies
2.6k
views
Tutorial: Video-tutorials: How to get started using EaSeq for interactive ChIP-seq data visualization and exploration (Windows)
ChIP-Seq visualization EaSeq Tutorial Windows
4.9 years ago by Mads Lerdrup ▴ 450
30
votes
14
replies
12k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
install genome music linux smg Tutorial
4.5 years ago by Cyriac Kandoth 5.5k
17
votes
13
replies
1.3k
views
Tutorial: Screen shots of text (please don't)!
meta Forum Tutorial
4.0 years ago by Michael Dondrup 48k
328 results • Page 1 of 7
Recent Votes
Answer: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens
Answer: Tool to find chromosome specific repeats
Answer: What Is The Total Size Of Hgdownload.Cse.Ucsc.Edu/Gbdb/Mm9
Comment: correct way of analyzing cell proportions in singlecell data
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Recent Replies
Comment: Extracting only tumor samples from Single cell RNASeq by jared.andrews07 9.1k
You need pre-defined variants for Vartrix. Typically it's used in conjuction with WGS/WES from bulk tissue to look for clonal variants in d…
Comment: Cell composition in each condition of single cell data by paria.alipour ▴ 20
Oh, I'm sorry. I already posted it in here the https://www.biostars.org/p/457243/#9464486. I've added the images
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens by Quanyou • 0
This seems OK when one gene generates only one transcirpt. But when one gene has multiple transcripts, these code would return a table wher…
Comment: How to convert Transcripts ID of rhesus monkey to Transcripts ID of homo sapiens by Quanyou • 0
This seems feasible. But I want to convert tens of thousands of transcript IDs. Could you tell me how can I make it through sequene search?
Answer: bbmap, mapq and uniquelly mapped reads filtering by GenoMax 99k
Many threads exist that show how to extract uniquely mapped reads. Here are a couple of examples:<br> https://www.biostars.org/p/276216/#27…
Comment: Cell composition in each condition of single cell data by rpolicastro 5.1k
The images seem to be missing from your post
Comment: Limma experiment design and making contrasts by kra277 • 0
Thank you very much for this. Much appreciated.
Comment: Limma experiment design and making contrasts by Kevin Blighe 72k
Hi, these follow the same principles as formulae used in regression modelling, so, you may want to focus on that (when searching). What lim…
Comment: Limma experiment design and making contrasts by kra277 • 0
That is very insightful. Thank you very much for the answer. Also, if I may ask, could you please point me to the articles for understandin…
Comment: Keep values from VCF file into Ensembl VEP annotation by brunobsouzaa ▴ 510
Thanks Man... I've wroten a simple awk command for this task! Everything is working fine.
Comment: Raw read processing using trimmomatic by boczniak767 ▴ 740
Do you have exact command used by the author? I guess that not all details was presented in the paper. You can always ask the corresponding…
Comment: should stop codon be counted as part of CDS by sullis02 • 0
Your github page appears to live here now https://github.com/NBISweden/GAAS/blob/master/annotation/knowledge/gxf.md
Comment: How do I compare degree and betweenness centrality for different PPI networks? by Istvan Albert 87k
I am not all that knowledgeable of Cytoscapes features and scripting capabilities, but if it does not support that operation you can expo…
Comment: Creating reference genome for mapping and then selecting by Istvan Albert 87k
you would get the counts as you would get them in any other case, how do you know something maps to chromosome 1 of human genome? Because i…
Comment: How do I compare degree and betweenness centrality for different PPI networks? by gemmalouisebaldock ▴ 10
Thank you very much Istvan for the reply. Yes, by not consistent I mean that my results are highly variable. I have been able to change the…
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