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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 19 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 11.2 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 10 days ago by 39k • written 4.7 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 9.4 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 3 months 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 3 months 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 3 months 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
9.5k
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
9.0k
views
Tutorial: How to generate PCA plot and heatmaps in R
heatmap PCA RNA-Seq R
updated 8 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 17 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 10.3 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
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
20
votes
4
replies
8.2k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 8 weeks ago by 39k • written 6.7 years ago by ★ 4.2k
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 3 months 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 17 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 18 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 19 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 17 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 11.1 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
7.5k
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 24 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
17 days ago by Ram 39k
11
votes
7
replies
7.3k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 16 days ago by 39k • written 2.3 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 18 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
Recent Votes
Answer: How to sort gff3 according to chromosome order?
Answer: how to sort unique seq from fasta files
Answer: Make a BedGraph file
Answer: Finding Enhancers using Genomation library
A: Extracting N positions from fasta file
Comment: Gene enrichment analysis
Comment: Gene enrichment analysis
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Popular Question to bioinfo_ga ▴ 50
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Recent Replies
Comment: Getting same value for start and end position, "DNA methylation" by ATpoint 72k
That's a comment, not an answer, please use `ADD COMMENT`.
Comment: Getting same value for start and end position, "DNA methylation" by bioinfo_ga ▴ 50
Are you working on bisulphite kind of data or chipseq ????
Answer: How to calculate TPM from featureCounts output by bioinfo_ga ▴ 50
hi , You can use a python package rnanorm [https://pypi.org/project/rnanorm/]. The input required are your read count values from feature …
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by biofalconch ▴ 580
Hey, if you arelady have the barcodes, you could use samtools `samtools view -h -b -f CB:Z:TAAGAGATCCTATGTT > TAAGAGATCCTATGTT.bam` Hope…
Answer: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by biofalconch ▴ 580
Here is a code that should work, but just like everyone else in the comments I'm a little confused why would you need to separate them: …
Comment: Make a BedGraph file by kirillkirilenko ▴ 10
It works, thank you!
Comment: CNNScoreVariants Error by Pierre Lindenbaum 154k
check you have a complete environment for GATK , including the python module "keras". https://gatk.broadinstitute.org/hc/en-us/articles/360…
Comment: How to split a scRNA reads BAM or FASTQ file to a separate file for each cell by by Cathal • 0
Did you have any luck in splitting the BAM file based on the 10x cell barcode? I would like to split a BAM file based to only include 5 spe…
Answer: Getting same value for start and end position, "DNA methylation" by ATpoint 72k
genomation is based on GenomicRanges which uses 1-based coordinates. https://www.biostars.org/p/84686/ Since a single CpG has a length o…
Comment: Gene enrichment analysis by ATpoint 72k
I cannot speak for this package but I recommend clusterProfiler where the universe argument isindeed all tested genes so your background.
Answer: Finding Enhancers using Genomation library by ATpoint 72k
You cannot derive enhancers from methylation profiles. Enhancers are regulatory elements, and they either are methylated or not. There is l…
Answer: convert data frame with character column to data frame with integer column by Basti ★ 1.5k
Cross-posted and answered there : https://stackoverflow.com/questions/76388032/convert-data-frame-with-character-column-to-data-frame-with-…
Comment: Getting same value for start and end position, "DNA methylation" by Basti ★ 1.5k
Your question lacks precision, we do not know what you are talking about
Comment: Gene enrichment analysis by Meisam ▴ 180
If you want to find enrichment of your selected genes versus the superset of all genes detected, then yes you mean the background. And to d…
Comment: WGCNA Trait File Issues by LChart 2.6k
The NAs are coming from the fact that each 'Sample' (which I assume is a unique identifier for a sample) is not actually a number and so th…
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