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353 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 bam GEO
updated 5 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 29 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 7.7 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 4 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 4 weeks ago by 38k • written 10.0 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 16 days ago by 38k • written 5.4 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
123
replies
29k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 8 days ago by ★ 1.1k • 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 16 days ago by 38k • written 4.7 years ago by 70k
100
votes
6
replies
22k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 15 days ago by 38k • written 4.6 years ago by 16k
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
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 15 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 16 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 28 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 20 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 20 days ago by 38k • written 2.5 years ago by 2.9k
82
votes
21
replies
71k
views
13 follow
Tutorial: How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools samtools htslib
updated 5 weeks ago by ★ 2.9k • written 4.7 years ago by ▴ 540
82
votes
28
replies
28k
views
19 follow
Tutorial: How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor GenVisR Graphics R
updated 6 weeks ago by 38k • written 7.1 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 23 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
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 15 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 9.4 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 4 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 6 weeks ago by 38k • written 5.6 years ago by 84k
70
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 97k
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
68
votes
26
replies
24k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 27 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
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 15 days ago by 38k • written 5.5 years ago by 84k
64
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 16 days ago by 38k • written 4.1 years ago by 16k
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
52
replies
39k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 15 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 5 weeks ago by 38k • written 10.6 years ago by 97k
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
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
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 15 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 12 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
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
51
votes
3
replies
22k
views
Tutorial: Sam File Format - Lesser Known Tips And Tricks
sam
updated 4 weeks ago by 38k • written 10.2 years ago by ▴ 300
50
votes
3
replies
4.0k
views
Tutorial: [[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 15 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 5 weeks ago by 38k • written 10.6 years ago by 97k
353 results • Page 1 of 8
Recent Votes
A: pulling snps from vcf file using ids
pulling snps from vcf file using ids
how to retrieve mouse (mm10) gene information from Ensemble using Biomart inR
STARsolo config for 10x Chromium v1, v2, v3
Answer: How to remove unknown batch-batch effects from GEO datasets
Any tips in landing a bioinformatic job?
A: correlation between SCRNA-Seq and bulk RNAseq
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Recent Replies
Answer: Convert .bam file from version 1.6 to 1.4 by Istvan Albert 97k
I think that if you should be able to convert you BAM file to SAM with the current version of `samtools`, then you use an older version of …
Answer: ChIPseeker Warning Message by ATpoint 70k
That happens when you merge or compare GRanges objects that have different chromosomes in it. Either your input or the content from org.Mm.…
Comment: extract gene coordinates and TSS from gene list by Chironex ▴ 40
thank you, I was able to get the coordinates of the gene, but I need to extract the TSS and extend it to 1000 bp.
Answer: extract gene coordinates and TSS from gene list by Carlo Yague 8.3k
I'm not going to give you a complete answer, but you can start looking at this posts: https://www.biostars.org/p/147351/ And use the [R …
Comment: How to make "Custom annotation File" for GO analysis using TOPgo by Shred ★ 1.1k
Do not post screenshots: instead use some lines of input and the desired output.
Comment: Snakemake doesn't recognize output files even though they are created by Shred ★ 1.1k
Sorry but I'm not able to properly understand your scenario. Did your pipeline complete the dry run?
Comment: How to remove unknown batch-batch effects from GEO datasets by 2317711200 • 0
Thank you very much for your response.
Answer: How to remove unknown batch-batch effects from GEO datasets by Gordon Smyth ★ 5.6k
removeBatchEffect() wouldn't produce the outlier effect that you show on the right unless there was something seriously wrong with the batc…
Answer: How to get subset of a Seurat object based on metadata? by fracarb8 ▴ 940
To keep the subset call as clean as possible, you can: Idents(skin) <- "predicted_cell_type" cell_values <- c("0:CD8 T cell") …
Answer: How to remove unknown batch-batch effects from GEO datasets by 2317711200 • 0
R codes： library(tidyverse) ####数据获取#### #引文 #citation(package = "GEOquery") #数据提取 GSE53625_matrix<-GEOquery::getGEO(GEO = "GSE5362…
Answer: Any tips in landing a bioinformatic job? by iraun 5.9k
Hi Jorge! In addition to what has already been said, I found my first bioinformatics job in Spain (Barcelona), using this webpage: [http…
Comment: How to remove unknown batch-batch effects from GEO datasets by 2317711200 • 0
It is a great honor to receive your response. The data in question is sourced from GSE53625. While using arrayQualityMetrics to assess the…
Answer: Extract data from Signac RegionMatrix? by Chironex ▴ 40
object@assays$ATAC@positionEnrichment$my_region_matrix and also object@assays$ATAC@positionEnrichment$my_region_matrix$condit…
Comment: Any tips in landing a bioinformatic job? by ATpoint 70k
Great answer, narrowing it down the the key points!
Comment: How to remove unknown batch-batch effects from GEO datasets by ATpoint 70k
The righthand plot might be totally fine once you remove that one outlier on the left, try that first. The batch effect manifesting along P…
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