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233
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176
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78k
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Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq TCGA Survival Tutorial
updated 3 months ago by 36k • written 6.9 years ago by ★ 4.5k
122
votes
119
replies
23k
views
22 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
6 weeks ago by Kevin Blighe 81k
86
votes
95
replies
28k
views
23 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial 1000 genomes PCA PLINK
updated 6 weeks ago by • 0 • written 3.8 years ago by 81k
75
votes
70
replies
14k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment Tutorial david
updated 5 months ago by • 0 • written 4.4 years ago by 81k
139
votes
67
replies
38k
views
17 follow
Tutorial: Network plot from expression data in R using igraph
R Tutorial microarray RNA-Seq network
updated 8 months ago by ▴ 10 • written 4.6 years ago by 81k
113
votes
66
replies
35k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump ENA Fastq Tutorial
11 months ago by ATpoint 62k
72
votes
59
replies
20k
views
15 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes PCA VCF PLINK Tutorial
updated 8 months ago by • 0 • written 4.8 years ago by 81k
60
votes
49
replies
36k
views
22 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 13 months ago by 36k • written 5.7 years ago by ★ 3.2k
72
votes
48
replies
14k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
bwa alignment ngs tutorial Tutorial
updated 11 weeks ago by 36k • written 9.4 years ago by 33k
192
votes
47
replies
66k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
tutorial bioconductor microarray analysis tutorial Tutorial
updated 4 months ago by ▴ 10 • written 9.7 years ago by 19k
55
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 2.1 years ago by • 0 • written 4.8 years ago by ★ 1.4k
75
votes
40
replies
25k
views
23 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 3 months ago by 36k • written 8.7 years ago by ★ 7.5k
17
votes
40
replies
14k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
run easy orthomcl all-v-all mcl Tutorial
updated 19 months ago by ★ 1.9k • written 6.0 years ago by ▴ 160
269
votes
39
replies
150k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA download GEO bam
updated 8 weeks ago by 36k • written 7.8 years ago by 19k
147
votes
35
replies
55k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics Tutorial next-gen
updated 6 weeks ago by • 0 • written 9.6 years ago by ★ 1.6k
142
votes
34
replies
49k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
mutation maf tcga cancer music Tutorial
updated 6 weeks ago by 36k • written 9.2 years ago by 5.8k
264
votes
33
replies
82k
views
24 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 4 months ago by ▴ 100 • written 8.7 years ago by 19k
41
votes
33
replies
6.1k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation Tutorial
19 months ago by Ram 36k
76
votes
32
replies
13k
views
17 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
R pathway enrichment active subnetwork Tutorial
updated 16 months ago by ▴ 30 • written 4.0 years ago by ★ 1.2k
81
votes
27
replies
25k
views
18 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
GenVisR BioConductor R Graphics Tutorial
updated 6 months ago by • 0 • written 6.3 years ago by 19k
61
votes
26
replies
8.4k
views
11 follow
Tutorial: Generating consensus sequence from bam file
bam consensus fasta Tutorial
updated 13 months ago by ▴ 180 • written 3.3 years ago by 15k
63
votes
26
replies
9.9k
views
7 follow
Tutorial: Parallel processing in R
R Tutorial biocparallel mclapply foreach
2.6 years ago by Kevin Blighe 81k
11
votes
26
replies
3.2k
views
Tutorial: gene set filter/selection for training ab initio annotation tools
genome gene Tutorial
updated 11 months ago by ▴ 610 • written 2.9 years ago by ★ 7.1k
63
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 2.1 years ago by 36k • written 8.4 years ago by 93k
128
votes
25
replies
69k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 11 weeks ago by 36k • written 10.2 years ago by ★ 4.1k
58
votes
25
replies
34k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC TCGA Download methylation Tutorial
updated 3.6 years ago by 62k • written 5.9 years ago by ★ 9.1k
94
votes
25
replies
30k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality fastq trimming qc tutorial Tutorial
updated 3 months ago by 36k • written 9.8 years ago by 93k
9
votes
23
replies
7.6k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
orthomcl ubuntu linux mysql Tutorial
4.1 years ago by vimalkvn ▴ 310
141
votes
21
replies
28k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 7 weeks ago by 36k • written 7.5 years ago by ★ 1.6k
11
votes
20
replies
9.5k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
seurat single cell RNA-Seq TCR Tutorial
13 months ago by jared.andrews07 ★ 13k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
orthomcl mysql no root local Tutorial
updated 4 months ago by 36k • written 7.6 years ago by ▴ 580
86
votes
19
replies
29k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
classification microarray expression bioconductor Tutorial
updated 5.5 years ago by • 0 • written 8.7 years ago by 19k
51
votes
19
replies
40k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
chip-seq rna-seq bigwig visualization ucsc tutorial Tutorial
updated 6.4 years ago by ★ 9.1k • written 10.2 years ago by 10k
23
votes
19
replies
5.1k
views
10 follow
Tutorial: MutScan: Detect important mutations by scanning FastQ files directly
mutation fastq cancer target Tutorial
updated 4.4 years ago by • 0 • written 5.7 years ago by ★ 2.4k
70
votes
19
replies
9.3k
views
15 follow
Tutorial: Gene Set Enrichment Analysis
enrichment microarray Tutorial GSEA RNA-Seq
8 weeks ago by Hamid Ghaedi ★ 2.5k
42
votes
19
replies
6.8k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software tutorial Tutorial
9.3 years ago by Daniel Standage 4.0k
47
votes
19
replies
11k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
fastqc qualitycontrol tutorial Tutorial
updated 9.3 years ago by ▴ 140 • written 9.3 years ago by 93k
8
votes
17
replies
2.1k
views
Tutorial: Simple approach to RNA-seq (T-Bioinfo platform)
Tutorials RNA-seq alignment next-gen sequencing
6.7 years ago by elia.brodsky ▴ 340
15
votes
17
replies
5.3k
views
9 follow
Tutorial: Create de novo repeat library
Tutorial repeat annotation de-novo
updated 10 months ago by • 0 • written 2.6 years ago by ★ 7.1k
26
votes
17
replies
6.1k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 6 months ago by 36k • written 7.9 years ago by 5.8k
12
votes
17
replies
2.0k
views
Tutorial: How to find the mapping percentages for data deposited in the Zaire ebolavirus bioproject from the 2014 outbreak
ebola bwa Tutorial
7.0 years ago by Istvan Albert 93k
42
votes
16
replies
20k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
CNV varscan2 GISTIC copy-number Tutorial
written 6.8 years ago by ★ 2.3k
98
votes
16
replies
27k
views
18 follow
Tutorial: Heatmaps in R
Tutorial R heatmap
7 weeks ago by Jean-Karim Heriche 25k
69
votes
16
replies
58k
views
10 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools bcftools htslib Tutorial
updated 6 months ago by • 0 • written 3.9 years ago by ▴ 460
32
votes
16
replies
14k
views
10 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
classification tutorial Tutorial
5.2 years ago by Obi Griffith 19k
34
votes
15
replies
17k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
R TCGA GDC next-gen Tutorial
updated 3.3 years ago by ▴ 30 • written 5.7 years ago by ▴ 310
24
votes
15
replies
7.4k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
bioinformatics training tutorial Tutorial
3 months ago by Medhat 9.3k
34
votes
15
replies
3.9k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf Tutorial
updated 3 months ago by 36k • written 3.0 years ago by ★ 9.1k
57
votes
15
replies
9.8k
views
Tutorial: Which human reference genome should I use?
genome alignment assembly Tutorial
3.6 years ago by finswimmer 15k
30
votes
14
replies
14k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
install genome music linux smg Tutorial
5.7 years ago by Cyriac Kandoth 5.8k
348 results • Page 1 of 7
Recent Votes
Answer: ESTIMATE tumor purity
C: Run PHI-BLAST in BLAST+ standalone
Answer: Junior bioinformatician in italy
Junior bioinformatician in italy
A: Thoughts on switching from Biology to Bioinformatics
The Biostar Handbook. A bioinformatics e-book for beginners.
The Biostar Handbook. A bioinformatics e-book for beginners.
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Scholar to JACKY ▴ 10
Scholar to Marco Pannone ▴ 290
Popular Question to hasani.iut6 ▴ 70
Popular Question to el97004 ▴ 50
Scholar to Pierre Lindenbaum 146k
Popular Question to pifferdavide ▴ 100
Popular Question to Zahra ▴ 50
Recent Replies
Answer: ESTIMATE tumor purity by JACKY ▴ 10
Just in case anyone faces this problem in the future, here is the link for the updated `estimate package` on github: https://github.com/…
Answer: Exctract unmapped reads from BLAST by GenoMax 117k
> Is there a way to tell blast to output the unmapped reads into a > separate file? No there is not. You will need to use `-outfmt 7` whe…
Comment: Resfams Database usage by Neel ▴ 10
Hi, i have annotated genome by prokka and o want to search amr agaisnt resfams could you please tell me how to do it steps by steps.
Comment: Exctract unmapped reads from BLAST by Pierre Lindenbaum 146k
those are two distinct commands https://linux.die.net/man/1/comm and https://linux.die.net/man/1/join extract the names of your queries, s…
Comment: Exctract unmapped reads from BLAST by Pilar • 0
Thanks for answering :), sorry, I'm new at this. These are commands I should use when I launch Blast in terminal?
Comment: Exctract unmapped reads from BLAST by Pierre Lindenbaum 146k
have a look at `comm` or `join`.
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK by pifferdavide ▴ 100
Sorry I forgot to mention I used it in this loop, which worked with another plink file, but not with this 1KG file. for popfile in $(l…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK by chrchang523 9.3k
`--indv` takes a single ID, not a filename. So `--indv IDlist.txt` shouldn't work.
Answer: Quast Ouput by Ying • 0
The "# contigs 47484" is based on contig of size >= 500 bp (see the first line of your screenshot). The "# contigs (>= 0 bp)" is the raw nu…
Answer: SRA obtained metagenomic reads appears to corrupt - cannot work on SingleM by Mensur Dlakic ★ 19k
Not sure why: 1) you are splitting reads; 2) you are fixing reads when they seem fine. I suggest something like this instead after `prefetc…
Comment: Quick way to get a field such as QNAME from the last read in a bam file? by kalavattam ▴ 70
Thank you. Do you know of any strategies for non-coordinated-sorted bam files?
Comment: analyzing a single cell and searching for a specific gene using single cell data by jared.andrews07 ★ 13k
@rpolicastro gave you several helpful links for using the h5ad file, in addition to how to explore and plot data. The links in my answer al…
Comment: Computing allele frequencies per individual for a set of SNPs in PLINK by pifferdavide ▴ 100
I was able to run the --indv command successfully on a file with a bed file by simply listing the IDs in single column. However, with anoth…
Answer: Get nucleotide sequence of assembled RNA transcripts by tomas4482 ▴ 140
1. design a RNA-seq experiment specifically seuqencing non-coding RNA/circRNA sequencing. 2. subset to interested region -> extract chi…
Comment: gffcompare by linjc.xmu ▴ 30
Thanks. I revised it. Do you know how to achieve it?
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