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352 results • Page 1 of 8
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276
votes
39
replies
164k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA download GEO bam
updated 10 months ago by 38k • written 8.6 years ago by 20k
274
votes
33
replies
91k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 21 days ago by 38k • written 9.4 years ago by 20k
238
votes
176
replies
84k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 5 months ago by 38k • written 7.6 years ago by ★ 4.6k
194
votes
44
replies
68k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 10 weeks ago by 38k • written 10.5 years ago by 20k
146
votes
35
replies
58k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 26 days ago by 38k • written 10.3 years ago by ★ 1.6k
145
votes
34
replies
51k
views
17 follow
Tutorial: Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music cancer tcga mutation maf
updated 25 days ago by 38k • written 9.9 years ago by 5.9k
144
votes
68
replies
43k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 8 days ago by 38k • written 5.3 years ago by 84k
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 10 months ago by 38k • written 8.3 years ago by ★ 1.6k
136
votes
25
replies
75k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 11 months ago by 38k • written 10.9 years ago by ★ 4.2k
130
votes
122
replies
28k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 12 days ago by 38k • written 4.4 years ago by 84k
116
votes
66
replies
40k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 8 days ago by 38k • written 4.7 years ago by 70k
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 7 days ago by 38k • written 6.6 years ago by 26k
99
votes
8
replies
27k
views
8 follow
Tutorial: Guide to TCGA data
TCGA cancer tools RNA-Seq clinical Tutorial
updated 6.3 years ago by ▴ 250 • written 7.1 years ago by ★ 1.1k
98
votes
6
replies
22k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 7 days ago by 38k • written 4.5 years ago by 16k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 27 days ago by 38k • written 10.5 years ago by 96k
92
votes
105
replies
34k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 8 days ago by 38k • written 4.6 years ago by 84k
89
votes
19
replies
30k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray bioconductor expression classification
updated 20 days ago by 38k • written 9.4 years ago by 20k
83
votes
34
replies
15k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
active-subnetwork enrichment pathway R
updated 12 days ago by 38k • written 4.7 years ago by ★ 1.3k
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 5 weeks ago by 38k • written 7.0 years ago by 20k
81
votes
8
replies
7.8k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 15 days ago by 38k • written 8.8 years ago by 19k
81
votes
21
replies
70k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 4 weeks ago by ★ 2.9k • written 4.7 years ago by ▴ 530
81
votes
21
replies
14k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 12 days ago by 38k • written 2.4 years ago by 2.9k
79
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 22 days ago by 38k • written 9.7 years ago by 11k
78
votes
41
replies
28k
views
24 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 3 months ago by • 0 • written 9.4 years ago by ★ 7.7k
76
votes
13
replies
14k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 17 months ago by 38k • written 8.8 years ago by 19k
75
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 7 days ago by 38k • written 5.1 years ago by 84k
74
votes
13
replies
65k
views
10 follow
Tutorial: Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r cancer classification
updated 4 months ago by 38k • written 9.3 years ago by ★ 1.2k
73
votes
14
replies
14k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 5 weeks ago by 38k • written 9.8 years ago by 9.5k
72
votes
48
replies
15k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 26 days ago by 38k • written 10.1 years ago by 33k
72
votes
60
replies
23k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes PLINK PCA VCF
updated 5 weeks ago by 38k • written 5.5 years ago by 84k
70
votes
5
replies
10k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 11 months ago by 38k • written 9.0 years ago by ★ 1.8k
69
votes
3
replies
34k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 16 months ago by 38k • written 8.7 years ago by 96k
68
votes
26
replies
24k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 19 days ago by 38k • written 9.1 years ago by 96k
67
votes
6
replies
24k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 27 days ago by 38k • written 10.6 years ago by 96k
65
votes
9
replies
47k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 6 weeks ago by 38k • written 9.7 years ago by ★ 3.0k
64
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 8 days ago by 38k • written 4.0 years ago by 16k
64
votes
5
replies
6.7k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 5 months ago by 38k • written 7.6 years ago by 12k
64
votes
26
replies
11k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 7 days ago by 38k • written 5.5 years ago by 84k
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 13 months ago by 38k • written 8.4 years ago by ★ 2.3k
60
votes
6
replies
8.9k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 22 days ago by 38k • written 9.6 years ago by 9.5k
60
votes
52
replies
39k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 7 days ago by 38k • written 6.5 years ago by ★ 3.3k
60
votes
2
replies
6.9k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 27 days ago by 38k • written 10.6 years ago by 96k
59
votes
43
replies
18k
views
18 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign pacbio arrow smrt-limk
updated 7 days ago by 38k • written 5.5 years ago by ★ 1.4k
59
votes
15
replies
11k
views
Tutorial: Which human reference genome should I use?
genome alignment assembly Tutorial
4.4 years ago by finswimmer 16k
58
votes
25
replies
36k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 4 days ago by 38k • written 6.6 years ago by ★ 9.3k
53
votes
5
replies
14k
views
6 follow
Tutorial: Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 5 months ago by 38k • written 9.3 years ago by ★ 1.2k
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 26 days ago by 38k • written 10.2 years ago by ▴ 300
51
votes
19
replies
41k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization bigwig chip-seq rna-seq
updated 29 days ago by 38k • written 10.9 years ago by 11k
50
votes
3
replies
4.0k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 7 days ago by 38k • written 4.2 years ago by 70k
48
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 27 days ago by 38k • written 10.6 years ago by 96k
352 results • Page 1 of 8
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Comment: Power analysis for patient samples
Comment: Snakemake vs Nextflow Upcoming bioinformatics Project
Comment: Snakemake vs Nextflow Upcoming bioinformatics Project
Answer: Creating a loop to mark duplicates using Picard
Transforming And Manipulating Color Space Reads
Comment: advice on course selection for a bioinformatics career.
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
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Recent Replies
Comment: Creating loop for read groups using Picard by Pierre Lindenbaum 153k
duplicate of https://www.biostars.org/p/9558127/
Comment: ClusterProfiler enrichKEGG – remove organism name in plots? by Mensur Dlakic ★ 23k
Is there a problem in using program version that produced your top plot? Unless there is known bug in a program, or a super-useful feature…
Answer: Need help teasing out insertions and deletions with bcftools stats file.vcf > fi by Afif Elghraoui • 0
Not in one step that I could find, but this works: deletions: ``` bcftools view --types indels --include 'ILEN<0' file.vcf | bcftools …
Comment: How to add gene information below the BSmooth result ? by diqixiaoyaoer ▴ 10
Thank you, sir. I have looked into your thesis. It's really great. I may have a try on Gviz if I don't have any idea about my question.
Comment: Snakemake vs Nextflow Upcoming bioinformatics Project by rackbersingh • 0
Brilliant, thanks for the advice, i think after looking into what the community has said I have invested into learning the groovy language …
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript by Juke34 7.7k
Change merge_loci to true
Comment: msigdbr returns the same genesets for mouse as in for human, by igor 13k
The addition of mouse-specific pathways to MSigDB is relatively recent. The package has not been updated to incorporate the latest version …
Comment: known-sites for Felis_catus_9.0 (GCA_000181335.4) by makarov • 0
Thank you, I also found vcf files https://ftp.ensembl.org/pub/release-109/variation/vcf/felis_catus/
Comment: Creating a loop to mark duplicates using Picard by Ram 38k
For someone new at shell scripts, you're doing really well at using shell variables and parameter expansion. Good going!
Comment: Creating a loop to mark duplicates using Picard by brandnewatthis • 0
Sorry, I am very new at this and am just learning my way around these symbols! Thanks for the help :)
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript by BioinfoBee • 0
its version 1.0.0. and installed using conda. How do I configure config.yaml file in such case?
Comment: Can I use abundance from Tximport to compare the expression level of transcript by Ram 38k
> Can I Yes. Should you? Probably not. There must be better, statistically more robust ways of quantifying based on biological replicates.
Answer: Problem generating a .vcf after upgrade of samtools and bcftools by GenoMax 127k
> I can't find the way using the man documentation of bcftools to get a > .vcf from a sorted .bam file. This should be all you need: https…
Comment: RNA-SEQ by Trivas ▴ 630
You should be able to do `fasterq-dump <SRR number> -O output_folder`
Comment: RNA-SEQ by GenoMax 127k
If you are trying to re-create an analysis and if it used both SRA# then you will need to get both. If you are simply learning/testing then…
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