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349 results • Page 1 of 7
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269
votes
39
replies
148k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA download GEO bam
updated 22 days ago by 36k • written 7.7 years ago by 19k
262
votes
33
replies
81k
views
24 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 3 months ago by ▴ 90 • written 8.6 years ago by 19k
233
votes
176
replies
77k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq TCGA Survival Tutorial
updated 9 weeks ago by 36k • written 6.8 years ago by ★ 4.5k
192
votes
47
replies
65k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
tutorial bioconductor microarray analysis tutorial Tutorial
updated 3 months ago by • 0 • written 9.6 years ago by 19k
147
votes
35
replies
55k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics Tutorial next-gen
updated 12 days ago by • 0 • written 9.5 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 9 days ago by 36k • written 9.1 years ago by 5.8k
141
votes
21
replies
28k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 16 days ago by 36k • written 7.4 years ago by ★ 1.6k
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 7 months ago by ▴ 10 • written 4.5 years ago by 81k
128
votes
25
replies
68k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 6 weeks ago by 36k • written 10.1 years ago by ★ 4.1k
122
votes
119
replies
22k
views
22 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
10 days ago by Kevin Blighe 81k
113
votes
66
replies
34k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump ENA Fastq Tutorial
10 months ago by ATpoint 60k
99
votes
8
replies
25k
views
8 follow
Tutorial: Guide to TCGA data
TCGA cancer tools RNA-Seq clinical Tutorial
updated 5.5 years ago by ▴ 250 • written 6.2 years ago by ★ 1.1k
98
votes
16
replies
27k
views
18 follow
Tutorial: Heatmaps in R
Tutorial R heatmap
16 days ago by Jean-Karim Heriche 25k
94
votes
25
replies
30k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality fastq trimming qc tutorial Tutorial
updated 10 weeks ago by 36k • written 9.7 years ago by 93k
91
votes
6
replies
19k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
snakemake conda workflow Tutorial
updated 18 months ago by ▴ 30 • written 3.7 years ago by 15k
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 5.4 years ago by • 0 • written 8.6 years ago by 19k
85
votes
95
replies
27k
views
23 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial 1000 genomes PCA PLINK
updated 11 days ago by • 0 • written 3.7 years ago by 81k
81
votes
8
replies
7.4k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
genomics workshop Tutorial lectures training
updated 11 days ago by 36k • written 7.9 years ago by 19k
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 5 months ago by • 0 • written 6.2 years ago by 19k
76
votes
13
replies
13k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 7 months ago by 36k • written 8.0 years ago by 19k
76
votes
32
replies
13k
views
17 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
R pathway enrichment active subnetwork Tutorial
updated 14 months ago by ▴ 30 • written 3.9 years ago by ★ 1.2k
75
votes
40
replies
25k
views
23 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 11 weeks ago by 36k • written 8.6 years ago by ★ 7.5k
75
votes
1
reply
49k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
tutorial Tutorial
written 8.9 years ago by 11k
75
votes
70
replies
14k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment Tutorial david
updated 3 months ago by • 0 • written 4.3 years ago by 81k
72
votes
13
replies
64k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification tutorial Tutorial
updated 3.7 years ago by 36k • written 8.5 years ago by ★ 1.2k
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 7 months ago by • 0 • written 4.7 years ago by 81k
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 6 weeks ago by 36k • written 9.3 years ago by 33k
70
votes
5
replies
9.8k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 6 weeks ago by 36k • written 8.1 years ago by ★ 1.8k
69
votes
3
replies
31k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 6 months ago by 36k • written 7.8 years ago by 93k
69
votes
19
replies
8.7k
views
15 follow
Tutorial: Gene Set Enrichment Analysis
enrichment microarray Tutorial GSEA RNA-Seq
25 days ago by Hamid Ghaedi ★ 2.5k
69
votes
16
replies
56k
views
10 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools bcftools htslib Tutorial
updated 5 months ago by • 0 • written 3.8 years ago by ▴ 460
68
votes
14
replies
12k
views
15 follow
Tutorial: List Of Bioinformatics Books
bioinformatics tutorial books Tutorial
updated 12 weeks ago by ▴ 40 • written 9.0 years ago by 9.3k
67
votes
6
replies
23k
views
7 follow
Tutorial: Rna-Seq Review Papers
papers rna-seq tutorial Tutorial
updated 6.3 years ago by • 0 • written 9.7 years ago by 93k
66
votes
9
replies
46k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
mapping samtools bwa reference Tutorial
updated 8 months ago by 36k • written 8.9 years ago by ★ 2.9k
63
votes
5
replies
6.3k
views
10 follow
Tutorial: Informatics of RNA-Seq.
RNA-Seq next-gen Tutorial
updated 6.5 years ago by 19k • written 6.8 years ago by 11k
63
votes
26
replies
9.7k
views
7 follow
Tutorial: Parallel processing in R
R Tutorial biocparallel mclapply foreach
2.5 years ago by Kevin Blighe 81k
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 2.0 years ago by 36k • written 8.3 years ago by 93k
63
votes
13
replies
12k
views
11 follow
Tutorial: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect GATK Picard Exome
updated 3 months ago by 36k • written 7.5 years ago by ★ 2.3k
61
votes
26
replies
8.1k
views
11 follow
Tutorial: Generating consensus sequence from bam file
bam consensus fasta Tutorial
updated 11 months ago by ▴ 180 • written 3.2 years ago by 15k
60
votes
2
replies
6.6k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
Tutorial papers
updated 8 months ago by 36k • written 9.7 years ago by 93k
60
votes
49
replies
36k
views
22 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 12 months ago by 36k • written 5.6 years ago by ★ 3.1k
60
votes
6
replies
8.5k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line tools bioinformatics Tutorial
3.4 years ago by Medhat 9.3k
57
votes
15
replies
9.6k
views
Tutorial: Which human reference genome should I use?
genome alignment assembly Tutorial
3.5 years ago by finswimmer 15k
57
votes
25
replies
34k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC TCGA Download methylation Tutorial
updated 3.5 years ago by 60k • written 5.8 years ago by ★ 9.0k
55
votes
41
replies
16k
views
16 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
arrow pbalign pacbio polishing smrt limk Tutorial
updated 2.0 years ago by • 0 • written 4.7 years ago by ★ 1.4k
52
votes
5
replies
13k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r tutorial Tutorial
updated 4.9 years ago by ▴ 130 • written 8.5 years ago by ★ 1.2k
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 6.3 years ago by ★ 9.0k • written 10.1 years ago by 10k
51
votes
3
replies
21k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam format tutorial Tutorial
updated 9.3 years ago by ★ 4.1k • written 9.4 years ago by ▴ 300
49
votes
3
replies
3.5k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
tutorial Tutorial how-to
2.3 years ago by ATpoint 60k
48
votes
7
replies
10k
views
7 follow
Tutorial: Genome Assembly Review Papers
papers assembly tutorial Tutorial
updated 9.3 years ago by 33k • written 9.7 years ago by 93k
349 results • Page 1 of 7
Recent Votes
A: Is it possible to run haplotypecaller in gnu parallel ?
Is it possible to run haplotypecaller in gnu parallel ?
A: Identifying De Novo Mutations from vcf files
Answer: Lasso regression and cross-validation on RNA seq dataset
A: How to combine multiple pheatmap figures and use common legend?
Comment: Help with kallisto-bustools: how to interpret the inspect.json output file
Answer: SARS-CoV-2 lineages complete reference genomes
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Recent Replies
Answer: Lasso regression and cross-validation on RNA seq dataset by Mensur Dlakic ★ 18k
It is not clear whether you have 192 datasets or 192 features in some undefined number of datasets, but either way cross validation is a sm…
Comment: SARS-CoV-2 lineages complete reference genomes by GenoMax 115k
I don't know if the following two resources are going to provide `reference` genomes. You may have to go to GSAID for that.
Answer: SARS-CoV-2 lineages complete reference genomes by GenoMax 115k
From EBI: https://www.covid19dataportal.org/sequences?crossReferencesOption=all ![EBI][1] [1]: /media/images/04dd9b11-77a8-4327-8…
Answer: Software to draw protein domains of proteins by cmdcolin ★ 2.1k
tools mentioned by other users are great, a couple more tools here https://cmdcolin.github.io/awesome-genome-visualization/?latest=true&tag…
Answer: SARS-CoV-2 lineages complete reference genomes by GenoMax 115k
At [**NCBI SARS-CoV-2**][1] resource page. Be sure to switch to `Nucleotide` tab and then click on pango lineage search. ![Pango][2] …
Answer: comparisons between 2 ChIP-seq datasets by jared.andrews07 ★ 13k
Honestly, I'd just eyeball the tracks in IGV. It's usually pretty apparent. If you want more objective measures, you could look at total…
Comment: data correaltion by Jeremy ▴ 130
FYI the cor.test() function will display a p-value in addition to the correlation coefficient.
Comment: Inflation in Imputed data by desicasares@gmail.com ▴ 10
Thank you for your answer...the populations I am using are Spanish, North European and Italian individuals. In the case of the Italians t…
Comment: MAF in R by malgorzata.sobczak07 • 0
You're the best! Thanks! :)
Comment: Help with kallisto-bustools: how to interpret the inspect.json output file by dsull ★ 3.0k
Correct, which is why you should load your output into R or python and filter your cells (i.e. do the "knee plot"). See the kallisto | bust…
Answer: MAF in R by Ram 36k
You can use `HardyWeinberg::maf` to calculate MAF from a vector of frequencies. You can create this vector of HOM/HET/HOM-ALT frequencies u…
Comment: MAF in R by malgorzata.sobczak07 • 0
Yeah, sorry :)
Comment: MAF in R by Ram 36k
Your code won't work. You'll need to quote the allele strings
Comment: The minor allele frequency by Negatyvna • 0
Yes, I would like to do the second option
Comment: NCBI tblastx remote by ailton • 0
Thanks a lot for the help. I managed to run it using its parameters, I also used other methods to run tblasx **$ tblastx -db databases/refe…
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