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346 results • Page 1 of 7
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273
votes
39
replies
159k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA download GEO bam
updated 7 months ago by 37k • written 8.3 years ago by 20k
273
votes
33
replies
88k
views
24 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 10 months ago by ▴ 100 • written 9.1 years ago by 20k
234
votes
176
replies
82k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 7 weeks ago by 37k • written 7.4 years ago by ★ 4.6k
194
votes
44
replies
67k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
tutorial bioconductor microarray analysis tutorial Tutorial
updated 8 weeks ago by 37k • written 10.2 years ago by 20k
146
votes
35
replies
57k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics Tutorial next-gen
updated 7 months ago by • 0 • written 10.0 years ago by ★ 1.6k
143
votes
34
replies
50k
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 7 months ago by 37k • written 9.6 years ago by 5.8k
142
votes
21
replies
28k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 7 months ago by 37k • written 8.0 years ago by ★ 1.6k
141
votes
68
replies
41k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
R Tutorial microarray RNA-Seq network
updated 5 months ago by • 0 • written 5.0 years ago by 84k
132
votes
25
replies
72k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 8 months ago by 37k • written 10.6 years ago by ★ 4.2k
128
votes
122
replies
26k
views
23 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
updated 3 months ago by • 0 • written 4.1 years ago by 84k
115
votes
66
replies
38k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera ENA fastq-dump Tutorial Fastq
5 months ago by ATpoint 66k
99
votes
8
replies
26k
views
8 follow
Tutorial: Guide to TCGA data
TCGA cancer tools RNA-Seq clinical Tutorial
updated 6.0 years ago by ▴ 250 • written 6.8 years ago by ★ 1.1k
98
votes
16
replies
29k
views
18 follow
Tutorial: Heatmaps in R
Tutorial R heatmap
7 months ago by Jean-Karim Heriche 26k
95
votes
6
replies
21k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
snakemake conda workflow Tutorial
updated 2.1 years ago by ▴ 50 • written 4.3 years ago by 15k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality fastq trimming qc tutorial Tutorial
updated 9 months ago by 37k • written 10.2 years ago by 96k
89
votes
104
replies
31k
views
24 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial 1000 genomes PCA PLINK
updated 8 weeks ago by ▴ 160 • written 4.3 years ago by 84k
89
votes
19
replies
30k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
classification microarray expression bioconductor Tutorial
updated 10 weeks ago by 37k • written 9.1 years ago by 20k
83
votes
34
replies
14k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
R pathway enrichment active subnetwork Tutorial
updated 4 months ago by 37k • written 4.5 years ago by ★ 1.3k
82
votes
28
replies
27k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
GenVisR BioConductor R Graphics Tutorial
updated 4 weeks ago by 123k • written 6.7 years ago by 20k
81
votes
8
replies
7.7k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
genomics workshop Tutorial lectures training
updated 7 months ago by 37k • written 8.5 years ago by 19k
79
votes
21
replies
12k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
enrichment microarray Tutorial GSEA RNA-Seq
updated 3 months ago by • 0 • written 2.1 years ago by 2.8k
78
votes
41
replies
27k
views
24 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 14 days ago by • 0 • written 9.1 years ago by ★ 7.6k
76
votes
13
replies
14k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 14 months ago by 37k • written 8.5 years ago by 19k
76
votes
2
replies
52k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
tutorial Tutorial
written 9.4 years ago by 11k
75
votes
70
replies
15k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment Tutorial david
updated 10 months ago by • 0 • written 4.8 years ago by 84k
74
votes
14
replies
13k
views
15 follow
Tutorial: List Of Bioinformatics Books
bioinformatics tutorial books Tutorial
updated 12 weeks ago by 37k • written 9.6 years ago by 9.4k
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 5 weeks ago by 37k • written 9.1 years ago by ★ 1.2k
73
votes
18
replies
65k
views
12 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools bcftools htslib Tutorial
updated 2 days ago by 37k • written 4.4 years ago by ▴ 500
72
votes
60
replies
22k
views
16 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes PCA VCF PLINK Tutorial
updated 6 days ago by • 0 • written 5.2 years ago by 84k
72
votes
48
replies
15k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
bwa alignment ngs tutorial Tutorial
updated 8 months ago by 37k • written 9.8 years ago by 33k
70
votes
5
replies
10k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 8 months ago by 37k • written 8.7 years ago by ★ 1.8k
69
votes
3
replies
33k
views
Tutorial: Revisiting the FastQC read duplication report
fastqc
updated 12 months ago by 37k • written 8.4 years ago by 96k
68
votes
26
replies
23k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
rna-seq tutorial Tutorial
updated 3 months ago by • 0 • written 8.8 years ago by 96k
67
votes
6
replies
24k
views
7 follow
Tutorial: Rna-Seq Review Papers
papers rna-seq tutorial Tutorial
updated 6.8 years ago by • 0 • written 10.3 years ago by 96k
66
votes
9
replies
47k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
mapping samtools bwa reference Tutorial
updated 15 months ago by 37k • written 9.4 years ago by ★ 3.0k
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 9 months ago by 37k • written 8.1 years ago by ★ 2.3k
63
votes
26
replies
11k
views
7 follow
Tutorial: Parallel processing in R
R Tutorial biocparallel mclapply foreach
3.1 years ago by Kevin Blighe 84k
63
votes
5
replies
6.6k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 7 weeks ago by 37k • written 7.3 years ago by 12k
62
votes
26
replies
9.8k
views
11 follow
Tutorial: Generating consensus sequence from bam file
bam consensus fasta Tutorial
updated 18 months ago by ▴ 180 • written 3.8 years ago by 15k
60
votes
49
replies
38k
views
22 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 19 months ago by 37k • written 6.2 years ago by ★ 3.3k
60
votes
2
replies
6.8k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
Tutorial papers
updated 15 months ago by 37k • written 10.3 years ago by 96k
60
votes
6
replies
8.8k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line tools bioinformatics Tutorial
updated 23 days ago by 37k • written 9.3 years ago by 9.4k
59
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 2.6 years ago by • 0 • written 5.2 years ago by ★ 1.4k
58
votes
25
replies
35k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC TCGA Download methylation Tutorial
updated 4.1 years ago by 66k • written 6.4 years ago by ★ 9.2k
57
votes
15
replies
11k
views
Tutorial: Which human reference genome should I use?
genome alignment assembly Tutorial
4.1 years ago by finswimmer 15k
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 10 weeks ago by 37k • written 9.0 years ago by ★ 1.2k
51
votes
19
replies
41k
views
6 follow
Tutorial: Visualizing Chip-Seq Data Using Ucsc [Bigwig]
chip-seq rna-seq bigwig visualization ucsc tutorial Tutorial
updated 4 months ago by 37k • written 10.6 years ago by 11k
51
votes
3
replies
21k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam format tutorial Tutorial
updated 9.9 years ago by ★ 4.2k • written 9.9 years ago by ▴ 300
50
votes
3
replies
3.8k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
tutorial Tutorial how-to
2.9 years ago by ATpoint 66k
48
votes
7
replies
10k
views
7 follow
Tutorial: Genome Assembly Review Papers
papers assembly tutorial Tutorial
updated 9.8 years ago by 33k • written 10.3 years ago by 96k
346 results • Page 1 of 7
Recent Votes
A: Extract base information from aligned reads in a sam file
A: Extract base information from aligned reads in a sam file
A: Combine paired-end fastq files
A: Why do the number of domains in these two orthologs differ? Why is hmmscan annot
SNPsift
C: How to sort a FASTA file and (its) BAM file in the same order?
A: What proportion of the (coding) genome is actually expressed at any given time?
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Scholar to Mensur Dlakic ★ 21k
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Recent Replies
Comment: Transform Data into DNA picture by anasjamshed1994 ▴ 120
what does genotype mean in rsid? What does it indicate?![rsid][1] [1]: /media/images/7638ed2f-7ed2-4cc0-8ce4-58ab0226
Comment: Any good tools for biological annotation of ChIP-seq broadpeak (H3K9me3, H3K27me by hiroyuki.kato.911 • 0
Thanks! I got it!
Answer: Inquiry related to processing multiple db file simulataneously by Pierre Lindenbaum 151k
how about calling `dbDisconnect` after `dbGetQuery` ?
Answer: Automated way to pull representative/RefSeq genome using full species name? by MirianT_NCBI ▴ 340
Hi Alex, You can use [NCBI Datasets][1]. `datasets` allows users to download genome and associated annotation files as a data package. I…
Comment: bedtools getfasta error: Error: malformed GFF entry at line 15. Coordinate detec by Pierre Lindenbaum 151k
but it's decoded AS a GFF/GTF file because bedtools can see columns 4 and 5 are integers. move columns 4 and 5 to columns 2 and 3 to create…
Comment: BioMart dropping and duplicating Ensembl IDs while retrieving corresponding gene by Matthias Zepper 2.4k
I already linked the MANE website above. Navigate to *Accessing MANE data* and download [this file][1]. It is an equivalence table and cont…
Comment: bedtools getfasta error: Error: malformed GFF entry at line 15. Coordinate detec by Simone • 0
It's not a GFF file, it's a TSV annotation file, output from BUSCO. The annotations are coordinates for BUSCO genes. I've tried using BEDOP…
Comment: What are Supplementary Reads? by cmdcolin ★ 2.5k
Large insertions or deletions can cause supplementary alignments to be created, even though it is still linear. But, minimap2 will try to a…
Comment: How to find rna strand direction before alignment? by swbarnes2 12k
OP said he didn't want to align. That script takes a bad and a bam as input.
Comment: GO enrichment analysis graphs after goseq: any easy solutions? by afsanarupa1 • 0
Please can you tell me details step by step how can these types of graphs be generated using output files from goseq as stated in trinity p…
Comment: What's Supplementary Reads? by Istvan Albert 96k
one concept the "linearity" of the alignment is important. A chimeric alignment is found to be "chimeric" if the entire read is represented…
Answer: How to find rna strand direction before alignment? by KoppesEA ▴ 80
[https://rseqc.sourceforge.net/][1] infer_experiment.py [1]: https://rseqc.sourceforge.net/ "RSEQC"
Answer: What's Supplementary Reads? by cmdcolin ★ 2.5k
I wrote a blogpost discussing some topics related to supplementary reads. Especially with long reads, supplementary reads are often "split …
Comment: For loop for aligning multiple paired end fastq files by Ram 37k
What did you have to do to get it working?
Comment: For loop for aligning multiple paired end fastq files by kcarery • 0
Thank you for your support, it is finally working
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