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231 results • Page 1 of 5
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276
votes
39
replies
165k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA bam GEO
updated 7 days ago by 38k • written 8.6 years ago by 20k
275
votes
33
replies
92k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 4 weeks 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 7.7 years ago by ★ 4.6k
194
votes
44
replies
68k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 11 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 5 weeks 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 5 weeks ago by 38k • written 10.0 years ago by 5.9k
144
votes
69
replies
43k
views
19 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 1 day ago by ▴ 10 • written 5.4 years ago by 85k
142
votes
21
replies
29k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 11 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 12 months ago by 38k • written 10.9 years ago by ★ 4.2k
130
votes
123
replies
29k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 10 days ago by ★ 1.1k • written 4.5 years ago by 85k
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 18 days ago by 38k • written 4.7 years ago by 71k
100
votes
6
replies
22k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 17 days ago by 38k • written 4.6 years ago by 16k
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 17 days ago by 38k • written 6.7 years ago by 26k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality qc trimming fastq
updated 5 weeks ago by 38k • written 10.5 years ago by 97k
92
votes
105
replies
34k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 18 days ago by 38k • written 4.6 years ago by 85k
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 4 weeks 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 22 days ago by 38k • written 4.8 years ago by ★ 1.3k
82
votes
21
replies
15k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 22 days ago by 38k • written 2.5 years ago by 2.9k
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 7 weeks ago by 38k • written 7.1 years ago by 20k
82
votes
21
replies
71k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 6 weeks ago by ★ 2.9k • written 4.7 years ago by ▴ 540
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 25 days ago by 38k • written 8.8 years ago by 19k
80
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 4 weeks ago by 38k • written 9.8 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 4 months ago by • 0 • written 9.5 years ago by ★ 7.7k
75
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 17 days ago by 38k • written 5.1 years ago by 85k
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 months ago by 38k • written 9.4 years ago by ★ 1.2k
73
votes
14
replies
14k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 7 weeks ago by 38k • written 9.9 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 5 weeks 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 7 weeks ago by 38k • written 5.6 years ago by 85k
70
votes
5
replies
10k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 12 months ago by 38k • written 9.0 years ago by ★ 1.8k
68
votes
26
replies
24k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 29 days ago by 38k • written 9.1 years ago by 97k
67
votes
6
replies
24k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
65
votes
9
replies
47k
views
7 follow
Tutorial: Reference Assembly - Mapping Reads To A Reference Genome
reference samtools mapping bwa
updated 7 weeks ago by 38k • written 9.8 years ago by ★ 3.0k
64
votes
26
replies
11k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 17 days ago by 38k • written 5.5 years ago by 85k
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 7.7 years ago by 12k
64
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 18 days ago by 38k • written 4.1 years ago by 16k
60
votes
6
replies
8.9k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 4 weeks ago by 38k • written 9.6 years ago by 9.5k
60
votes
2
replies
6.9k
views
Tutorial: Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
60
votes
52
replies
39k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 17 days ago by 38k • written 6.5 years ago by ★ 3.3k
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 17 days ago by 38k • written 5.5 years ago by ★ 1.4k
58
votes
25
replies
36k
views
15 follow
Tutorial: Protocol To Downlad TCGA Data From GDC
GDC methylation TCGA
updated 14 days ago by 38k • written 6.7 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 6 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 5 weeks 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 5 weeks ago by 38k • written 11.0 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 17 days ago by 38k • written 4.2 years ago by 71k
48
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 5 weeks ago by 38k • written 10.6 years ago by 97k
47
votes
19
replies
12k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 11 weeks ago by 38k • written 10.1 years ago by 97k
45
votes
14
replies
59k
views
10 follow
Tutorial: Using R in Conda
R
updated 17 days ago by 38k • written 2.7 years ago by ▴ 690
45
votes
2
replies
35k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 6 weeks ago by 38k • written 11.0 years ago by ▴ 540
44
votes
1
reply
6.2k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger RNA-seq
updated 7 weeks ago by 38k • written 2.5 years ago by 71k
43
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 29 days ago by 38k • written 9.2 years ago by 5.9k
231 results • Page 1 of 5
Recent Votes
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
Talk from Aaron Lun on Orchestrating Single-Cell Analysis With Bioconductor
SSPACE for scaffolding
Answer: Snakemake workflow for trimmomatic
Answer: How to remove duplicate reads after ONT basecalling from fastq.gz files
A: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p
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Recent Replies
Comment: TCGA-BRCA tissue and RNAseq problem by pinheirofabiano ▴ 10
Go to https://portal.gdc.cancer.gov > Exploration > select TCGA and the cancer type you want > select case ID to download the files and hav…
Answer: Snakemake workflow for trimmomatic by antoine.fauchois92 • 0
Thank you very much for your reply ! It's working now !
Comment: Dependent p values by Eliza ▴ 20
@lchart I'm sorry for asking another of questions but I'm new to this field , can you please explain a little more how to use SKAT , saige…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
similar question [here][1], [here][2] and [here][3] [1]: https://support.bioconductor.org/p/54838/ [2]: https://support.bioconductor.…
Comment: How to deal with the probe id mapping to multiple gene ids? by dare_devil ★ 1.7k
@genomax I have used the same platform file only. If you look at probe id and their corresponding `Gene Symbol` or `ENTREZ_GENE_ID` you can…
Comment: How to deal with the probe id mapping to multiple gene ids? by GenoMax 127k
Where are you seeing this? [Platform file for this array][1] on GEO has these names uniquely assigned. [1]: https://www.ncbi.nlm.nih.go…
Comment: My keys are all ENSEMBL, but R says they are not valid keys for ENSEMBL by rpolicastro 11k
`Org.Mm.eg.db` is the mouse organism database, but your ENSEMBL IDs are for human genes. Mouse ensembl ids start with `ENSMUSG`. You proba…
Comment: Snakemake doesn't recognize output files even though they are created by DdogBoss • 0
Yes, it completed the dry run. What other information do you need?
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Based on my personal thought, I think the se from LDSC output probably needs to be transferred using Delta method based on Fisher transform…
Comment: LDSC correlation calculate confidence intervals by YL ▴ 10
Hi, Are you able to find an answer for this? I have the exact question! YL
Answer: Gene duplicate by ATpoint 71k
Use use ensembID_geneName as gene identifier to avoid that. These duplicate names exist as genes so removing them is somewhat not really da…
Comment: Gene duplicate by Ram 38k
> some Ensembl IDs that are the same Please show us some examples.
Comment: R package for functional enrichment and depletion analysis by rpolicastro 11k
What you're describing is a simulation of the hypergeometric test, so if you want an exact solution you could use the function `fora` from …
Comment: How to remove duplicate reads after ONT basecalling from fastq.gz files by Darrenjdd • 0
Perfect! Thank you!
Comment: Why Chip-seq data cross correlation plot has fragment_lenth cross correlation p by Daniel • 0
Hi, I am wondering if you ever got an answer for this question. Also, I am curious why it is true that "All the reads coming from one end…
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