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114 results • Page 1 of 3
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273
votes
39
replies
162k
views
29 follow
Tutorial: How to download raw sequence data from GEO/SRA
fastq SRA download GEO bam
updated 9 months ago by 37k • written 8.4 years ago by 20k
234
votes
176
replies
83k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 3 months ago by 37k • written 7.5 years ago by ★ 4.6k
194
votes
44
replies
67k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 27 days ago by 37k • written 10.4 years ago by 20k
146
votes
35
replies
57k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics Tutorial next-gen
updated 9 months ago by • 0 • written 10.2 years ago by ★ 1.6k
143
votes
34
replies
51k
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 months ago by 37k • written 9.8 years ago by 5.8k
142
votes
21
replies
28k
views
12 follow
Tutorial: A few words for R beginners
Swirl R
updated 9 months ago by 37k • written 8.2 years ago by ★ 1.6k
142
votes
68
replies
42k
views
18 follow
Tutorial: Network plot from expression data in R using igraph
R Tutorial microarray RNA-Seq network
updated 7 months ago by • 0 • written 5.2 years ago by 84k
136
votes
25
replies
74k
views
14 follow
Tutorial: Piping With Samtools, Bwa And Bedtools
unix samtools bwa bedtools
updated 10 months ago by 37k • written 10.8 years ago by ★ 4.2k
128
votes
122
replies
27k
views
23 follow
Tutorial: Survival analysis with gene expression
survival analysis cox geo gene expression Tutorial
updated 5 months ago by • 0 • written 4.3 years ago by 84k
115
votes
66
replies
39k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera ENA fastq-dump Tutorial Fastq
7 months ago by ATpoint 68k
98
votes
16
replies
29k
views
18 follow
Tutorial: Heatmaps in R
Tutorial R heatmap
9 months ago by Jean-Karim Heriche 26k
94
votes
25
replies
31k
views
11 follow
Tutorial: Fastq Quality Control Shootout
quality fastq trimming qc tutorial Tutorial
updated 6 days ago by 37k • written 10.4 years ago by 96k
92
votes
105
replies
32k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
Tutorial 1000 genomes PCA PLINK
updated 6 days ago by ▴ 40 • written 4.4 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 4 months ago by 37k • written 9.3 years ago by 20k
83
votes
34
replies
15k
views
21 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
R pathway enrichment active subnetwork Tutorial
updated 6 months ago by 37k • written 4.6 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 3 months ago by 125k • written 6.9 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 9 months ago by 37k • written 8.7 years ago by 19k
79
votes
21
replies
13k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment Tutorial GSEA RNA-Seq
7 weeks ago by Hamid Ghaedi 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 10 weeks ago by • 0 • written 9.3 years ago by ★ 7.6k
78
votes
2
replies
53k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
tutorial Tutorial
written 9.6 years ago by 11k
77
votes
19
replies
68k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
samtools bcftools htslib Tutorial
updated 14 days ago by • 0 • written 4.5 years ago by ▴ 530
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 3 months ago by 37k • written 9.2 years ago by ★ 1.2k
74
votes
14
replies
13k
views
15 follow
Tutorial: List Of Bioinformatics Books
bioinformatics tutorial books Tutorial
updated 4 months ago by 37k • written 9.7 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?
bwa alignment ngs tutorial Tutorial
updated 10 months ago by 37k • written 10.0 years ago by 33k
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 9 weeks ago by • 0 • written 5.4 years ago by 84k
70
votes
5
replies
10k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 10 months ago by 37k • written 8.8 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 tutorial Tutorial
updated 12 days ago by 37k • written 9.0 years ago by 96k
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 11 months ago by 37k • written 8.3 years ago by ★ 2.3k
63
votes
5
replies
6.7k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 3 months ago by 37k • written 7.5 years ago by 12k
60
votes
52
replies
38k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 4 weeks ago by 37k • written 6.4 years ago by ★ 3.3k
60
votes
6
replies
8.8k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line tools bioinformatics Tutorial
updated 11 weeks ago by 37k • written 9.5 years ago by 9.5k
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 4 months ago by 37k • written 9.2 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 6 months ago by 37k • written 10.8 years ago by 11k
47
votes
19
replies
12k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 27 days ago by 37k • written 9.9 years ago by 96k
45
votes
14
replies
53k
views
10 follow
Tutorial: Using R in Conda
R Tutorial
updated 3 months ago by ▴ 20 • written 2.6 years ago by ▴ 690
42
votes
16
replies
21k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 6 months ago by 37k • written 7.4 years ago by ★ 2.3k
41
votes
1
reply
5.9k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
edger tutorial rna-seq
7 weeks ago by ATpoint 68k
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell Tutorial flow-cytometry
10 weeks ago by Ahill ★ 1.9k
37
votes
8
replies
8.7k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer Tutorial R methylation
updated 9 weeks ago by ★ 1.1k • written 2.3 years ago by 2.8k
34
votes
4
replies
5.5k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 11 weeks ago by 37k • written 7.6 years ago by ▴ 370
34
votes
15
replies
4.8k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf Tutorial
updated 11 months ago by 37k • written 3.6 years ago by ★ 9.2k
31
votes
9
replies
22k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda Tutorial
updated 8 months ago by • 0 • written 2.5 years ago by ▴ 140
30
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
bioinformatics pipeline python tutorial Tutorial
updated 9 months ago by 37k • written 8.8 years ago by ▴ 800
29
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 4 months ago by 37k • written 10.8 years ago by 96k
27
votes
0
replies
2.5k
views
Tutorial: Building Docker images
singularity docker container
6 months ago by ATpoint 68k
26
votes
17
replies
6.5k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 4 months ago by 37k • written 8.5 years ago by 5.9k
24
votes
15
replies
7.8k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
bioinformatics training tutorial Tutorial
10 months ago by Medhat 9.5k
24
votes
10
replies
55k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
Tutorial error software R
updated 8 months ago by • 0 • written 22 months ago by ★ 1.3k
22
votes
1
reply
3.0k
views
Tutorial: Introduction To R Course Materials Available
R
updated 4 weeks ago by 37k • written 10.8 years ago by 26k
21
votes
2
replies
3.4k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 5 months ago by ▴ 40 • written 21 months ago by 7.5k
114 results • Page 1 of 3
Recent Votes
Answer: Dealing with missing (NA) values in my 450K methylation array dataset
What type of database does gnomAD use?
What type of database does gnomAD use?
Answer: What type of database does gnomAD use?
Answer: What type of database does gnomAD use?
Answer: What type of database does gnomAD use?
Answer: How can I convert this pairwise format to fasta?
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Recent Replies
Comment: how to get an average ROC curve after 10-fold cross validation in r by Mensur Dlakic ★ 22k
I have no idea what cutoff is in this context, nor what you mean by `original` values. I don't know how you got those values for means. I …
Comment: Protein protein interactions by Mensur Dlakic ★ 22k
This is not a trivial calculation nor a simple sequence comparison like with BLAST, so it may take a while. Besides, there could be hundred…
Comment: snakemake Unexpected keyword bam in rule definition by Wayne ★ 1.6k
Any chance it is an indentation issue that isn't caused by what you aren't sharing here? See [here](https://groups.google.com/g/snakemake/c…
Comment: Size of two scRNA-Seq conditions by rpolicastro 11k
More important would be the cell QC stats (such as reads per cell and number of unique features detected per cell), the number of cells per…
Answer: What type of database does gnomAD use? by Jeremy Leipzig 21k
If you primarily want a variant warehouse that supports genomic region and sample queries at biobank scale, you should look into [TileDB-VC…
Answer: Dealing with missing (NA) values in my 450K methylation array dataset by Basti ★ 1.3k
You could omit the NA values : `pca <- prcomp(na.omit(t(exprs(GSE65820))))`
Comment: Virtual box by Ram 37k
This post does not fit the theme of this forum.
Comment: Filter InterProScan output for a specific function by jv ▴ 780
I imagine you can filter on things like E.C. numbers and domain names using `bash`, `awk`, `R`, or some other code.
Comment: How to find the most frequent alternative-splicing event from DEXSEQ data? by STARDUST • 0
I will try both rMATS and SUPPA for categorising changes. For the specific exons, i'm expecting the last exons should be affected. That is …
Answer: snp Caenorhabditis elegans by GenoMax 125k
See: https://www.elegansvariation.org/data/release/20220216
Answer: want the codes for cuffdiff , NIOSeq , bayseq to perform DEGs. by jv ▴ 780
- NOISeq <https://www.bioconductor.org/packages/release/bioc/vignettes/NOISeq/inst/doc/NOISeq.pdf> - Cuffdiff <http://cole-trapnell-lab.gi…
Comment: fastqc: Per base sequence content by jv ▴ 780
I think this is to be expected based a report I was able to find online <https://uu.diva-portal.org/smash/get/diva2:1608120/FULLTEXT01.pd…
Comment: fastqc: Per base sequence content by GenoMax 125k
Unless the kit directions tell you to remove remove the initial 10-15 bp you may as well leave them alone. Data should align would be my in…
Comment: RNA Editing data from RNA-seq by Genetics • 0
Thank you so much for your kind reply and for helping a bioinformatics beginner like me. Can I use **bowtie2** tools for allignment and th…
Comment: fastqc: Per base sequence content by khoojj • 0
Yes, I have proceed with analysis but I wonder if it is necessary to remove the first 10 or so bp from the reads. I have checked that NEBN…
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