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323 results • Page 2 of 7
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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 8 months ago by 39k • written 9.5 years ago by ★ 1.2k
15
votes
5
replies
14k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 8 weeks ago by 39k • written 7.0 years ago by 20k
16
votes
11
replies
13k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 11 weeks ago by 39k • written 6.6 years ago by ★ 4.6k
11
votes
7
replies
13k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 16 days ago by 39k • written 5.7 years ago by 85k
20
votes
4
replies
13k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 3 months ago by 39k • written 10.2 years ago by 20k
16
votes
7
replies
13k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 11 weeks ago by 39k • written 4.0 years ago by ▴ 310
47
votes
19
replies
12k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 4 months ago by 39k • written 10.3 years ago by 98k
16
votes
0
replies
12k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 3 months ago by 39k • written 11.1 years ago by 9.9k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 12 weeks ago by 39k • written 8.5 years ago by ▴ 580
44
votes
3
replies
12k
views
Tutorial: A Wet-Lab Guide to 'what I wish I had known' for Computational Biology
bioinformatics computational-biology
updated 8 weeks ago by 39k • written 7.2 years ago by ★ 3.2k
59
votes
15
replies
12k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 7 days ago by 39k • written 4.6 years ago by 16k
12
votes
20
replies
12k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 11 weeks ago by 39k • written 4.0 years ago by ★ 14k
64
votes
26
replies
12k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 11 weeks ago by 39k • written 5.7 years ago by 85k
18
votes
3
replies
12k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 10 months ago by 39k • written 7.3 years ago by ★ 9.3k
65
votes
26
replies
11k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 11 weeks ago by 39k • written 4.2 years ago by 16k
43
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 3 months ago by 39k • written 9.3 years ago by 5.9k
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 12 weeks ago by 39k • written 5.5 years ago by ▴ 750
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 10 months ago by 39k • written 7.3 years ago by ★ 1.8k
48
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 12 weeks ago by 39k • written 9.1 years ago by ★ 1.9k
30
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 12 weeks ago by 39k • written 9.1 years ago by ▴ 800
8
votes
9
replies
10k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 12 weeks ago by 39k • written 9.1 years ago by ★ 1.8k
38
votes
8
replies
10k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 12 weeks ago by 39k • written 2.7 years ago by 2.9k
3
votes
13
replies
10k
views
Tutorial: Merging multiple vcf files into Single vcf file
merge vcf bcftools
updated 12 weeks ago by 39k • written 4.3 years ago by ▴ 140
31
votes
6
replies
9.4k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 11 weeks ago by 39k • written 3.0 years ago by 85k
10
votes
4
replies
9.4k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 11 weeks ago by 39k • written 3.9 years ago by 4.8k
60
votes
6
replies
9.0k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 3 months ago by 39k • written 9.8 years ago by 9.6k
14
votes
0
replies
8.9k
views
Tutorial: How to generate PCA plot and heatmaps in R
heatmap PCA RNA-Seq R
updated 7 weeks ago by 39k • written 6.7 years ago by ★ 2.9k
9
votes
23
replies
8.6k
views
7 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 14 days ago by 39k • written 5.4 years ago by ▴ 310
19
votes
4
replies
8.5k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 3 months ago by 39k • written 10.2 years ago by 98k
16
votes
5
replies
8.5k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 3 months ago by 39k • written 10.7 years ago by 20k
20
votes
0
replies
8.4k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 3 months ago by 39k • written 10.8 years ago by 98k
20
votes
4
replies
8.2k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 7 weeks ago by 39k • written 6.7 years ago by ★ 4.2k
9
votes
0
replies
8.2k
views
Tutorial: Installing And Running Ncbi Blast
blast
updated 3 months ago by 39k • written 11.2 years ago by ▴ 540
24
votes
15
replies
8.1k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 3 months ago by 39k • written 10.4 years ago by 9.6k
81
votes
8
replies
8.0k
views
6 follow
Tutorial: Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop lectures genomics training
updated 12 weeks ago by 39k • written 9.0 years ago by 19k
3
votes
3
replies
7.9k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 14 days ago by 39k • written 5.4 years ago by ▴ 100
2
votes
2
replies
7.8k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 15 days ago by 39k • written 5.5 years ago by ★ 2.4k
10
votes
1
reply
7.7k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 16 days ago by 39k • written 5.7 years ago by ▴ 110
12
votes
5
replies
7.7k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 8 weeks ago by 39k • written 7.0 years ago by ★ 9.3k
0
votes
0
replies
7.6k
views
Tutorial: Multicollinearity VIF (Variance Inflation Factor) Analysis in Panel data EVIEWS 9
R eviews
updated 14 days ago by 39k • written 5.4 years ago by ▴ 10
6
votes
1
reply
7.6k
views
Tutorial: Expression Analysis Of Rna-Seq Experiments With Tophat And Cufflinks
tophat RNA-seq cufflinks
updated 3 months ago by 39k • written 11.0 years ago by 98k
16
votes
11
replies
7.5k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
11 weeks ago by Ram 39k
18
votes
22
replies
7.4k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 11 weeks ago by 39k • written 3.5 years ago by 7.9k
11
votes
2
replies
7.4k
views
Tutorial: Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome plot coverage samtools
updated 21 days ago by 39k • written 6.2 years ago by ★ 1.5k
45
votes
28
replies
7.3k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
14 days ago by Ram 39k
11
votes
7
replies
7.2k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 13 days ago by 39k • written 2.2 years ago by ▴ 300
42
votes
19
replies
7.2k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 3 months ago by 39k • written 10.3 years ago by 4.1k
20
votes
2
replies
7.2k
views
Tutorial: Creating a karyotype plot with genes using karyoploteR
karyoploteR visualization R genome
updated 15 days ago by 39k • written 5.5 years ago by ★ 3.4k
6
votes
4
replies
7.0k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 3 months ago by 39k • written 10.2 years ago by 11k
323 results • Page 2 of 7
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Answer: Help with running ATAC using Encode pipeline
Answer: How to extract haplotype data from phased bcf files
Answer: How to extract haplotype data from phased bcf files
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Comment: ggsave() bug in ggplot2?
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Recent Replies
Comment: All combinations of two columns R by Basti ★ 1.5k
Where are you stuck ? You need to give a reproducible example if you want a precise answer
Comment: How to extract haplotype data from phased bcf files by Lynne-95 • 0
Thanks that worked perfectly!
Answer: How to extract haplotype data from phased bcf files by Pierre Lindenbaum 154k
use %TGT (translated genotype) $ bcftools query -f '[%CHROM %POS %TGT\n]'
Comment: convert data frame with character column to data frame with integer column by Basti ★ 1.5k
You would better give an example with values because we don't know what is in each variable so we cannot give you a precise code, but seems…
Comment: RNASeq gene labeling and mRNA filter from bulkRNA data. by ATpoint 72k
This information is annotated in GTF files. You can get them for almost every annotated species from Ensembl. There is a column `gene_bioty…
Answer: DE genes across multiple scRNAseq clusters-are they significantly enriched? by ATpoint 72k
First of all, with thousands of DEGs you might want to choose a DE framework that allows testing against a fold change threshold, such as `…
Comment: PacBio Pipeline and Tools for Variant Call by Kiran ▴ 80
Thanks a lot William, I am Clear now
Comment: The famous WGS dataset, Ashkenazi Trio? by cmdcolin ★ 3.0k
what is valuable information to you
Answer: Why weblogo of biopython doesn't work? by minakshiboruahassam • 0
The weblogo3 application is giving same file even if u run the scripts separately on python standalone or whatever. The weblogo command is …
Answer: Make a BedGraph file by rfran010 ▴ 90
I would suggest bedtools makewindows to generate your 3,000bp bins then bedtools coverage to generate fraction of repeats over your windows…
Answer: What is the best way to clean bulk RNA-seq data? by rfran010 ▴ 90
Honestly, I am a fan of visualizing to select a threshold since these can depend on the specific experiment. I would even just run standard…
Answer: Help with running ATAC using Encode pipeline by rfran010 ▴ 90
Read all instructions carefully Specifically, this info is under the "Input JSON file specification" section with details in the followin…
Answer: BioInformatics, Software by rfran010 ▴ 90
There have been some good suggestions, but it seems like you may be asking one of two questions, either (1) how to do bioinformatics? or (2…
Answer: Genome assembly statistical tools by Bryan • 0
I'll follow up what a few others have mentioned, but I like stats.sh within the BBTools package for raw assembly stats. I'll then polish my…
Comment: how to design a guide RNA by rfran010 ▴ 90
I agree this is very basic CRISPR mechanism and you'd be better off reading sites that could explain better than me. However, there is a lo…
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