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383 results • Page 2 of 8
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72
votes
48
replies
17k
views
15 follow
Tutorial: For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs alignment bwa
updated 9 months ago by 41k • written 10.8 years ago by 33k
35
votes
17
replies
16k
views
12 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 6 months ago by 136k • written 10.0 years ago by 20k
30
votes
14
replies
16k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 9 months ago by 41k • written 10.8 years ago by 6.0k
75
votes
14
replies
15k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 9 months ago by 41k • written 10.5 years ago by 9.7k
16
votes
7
replies
15k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 8 months ago by 41k • written 4.5 years ago by ▴ 310
15
votes
5
replies
15k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 7 months ago by 41k • written 7.5 years ago by 20k
76
votes
13
replies
15k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 2.1 years ago by 41k • written 9.5 years ago by 19k
54
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 14 months ago by 41k • written 10.0 years ago by ★ 1.2k
16
votes
11
replies
14k
views
7 follow
Tutorial: retrieve full TCGA datasets from cBioportal with R
TCGA RNA-seq data-retrieval cBioportal R
updated 8 months ago by 41k • written 7.1 years ago by ★ 4.7k
11
votes
7
replies
14k
views
Tutorial: Removing rows with duplicate values based on 1 or more key values - linux awk
awk linux bash
updated 6 months ago by 41k • written 6.2 years ago by 86k
13
votes
3
replies
14k
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 3 months ago by ▴ 20 • written 6.7 years ago by ★ 1.6k
20
votes
4
replies
14k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 9 months ago by 41k • written 10.7 years ago by 20k
12
votes
20
replies
13k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 8 months ago by 41k • written 4.5 years ago by ★ 16k
63
votes
15
replies
13k
views
Tutorial: Which human reference genome should I use?
assembly genome alignment
updated 6 months ago by 41k • written 5.1 years ago by 16k
65
votes
26
replies
13k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 8 months ago by 41k • written 4.7 years ago by 16k
19
votes
3
replies
13k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 16 months ago by 41k • written 7.8 years ago by ★ 9.3k
47
votes
19
replies
13k
views
8 follow
Tutorial: Fastq Quality Control And Reporting - Aka Fastqc Versus The New Contenders
quality-control fastqc
updated 10 months ago by 41k • written 10.8 years ago by 99k
64
votes
13
replies
13k
views
11 follow
Tutorial: Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect GATK Picard Exome
updated 21 months ago by 41k • written 9.1 years ago by ★ 2.4k
64
votes
26
replies
13k
views
7 follow
Tutorial: Parallel processing in R
biocparallel mclapply foreach R
updated 8 months ago by 41k • written 6.2 years ago by 86k
8
votes
19
replies
13k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 8 months ago by 41k • written 9.0 years ago by ▴ 600
16
votes
0
replies
13k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 9 months ago by 41k • written 11.6 years ago by 10k
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 7 months ago by 41k • written 7.7 years ago by ★ 3.2k
39
votes
8
replies
12k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 8 months ago by 41k • written 3.2 years ago by 3.1k
15
votes
5
replies
12k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 8 months ago by 41k • written 6.0 years ago by ▴ 760
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 9 months ago by 41k • written 9.8 years ago by 6.0k
4
votes
13
replies
12k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 5 months ago by 41k • written 4.8 years ago by ▴ 140
28
votes
13
replies
12k
views
9 follow
Tutorial: How to get FASTQ reads from the Short Read Archive (SRA)
fastq sra
updated 22 months ago by ★ 1.3k • written 2.1 years ago by 99k
7
votes
2
replies
11k
views
Tutorial: Howto use NCBI programs behind a HTTP proxy
blast-plus HTTP-proxy SRA-toolkit
updated 16 months ago by 41k • written 7.8 years ago by ★ 1.8k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 8 months ago by 41k • written 9.6 years ago by ★ 1.9k
31
votes
6
replies
11k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 8 months ago by 41k • written 3.5 years ago by 86k
49
votes
7
replies
11k
views
7 follow
Tutorial: Genome Assembly Review Papers
assembly papers
updated 9 months ago by 41k • written 11.2 years ago by 99k
0
votes
0
replies
11k
views
Tutorial: Using PatMatch to search for nucleic and protein sequence patterns and integrate the results with Python/Jupyter for downstream analysis
Jupyter Python pattern
22 months ago by Wayne ★ 1.8k
70
votes
5
replies
11k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 20 months ago by 41k • written 9.6 years ago by ★ 1.8k
31
votes
8
replies
11k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 8 months ago by 41k • written 9.6 years ago by ▴ 810
8
votes
9
replies
11k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 8 months ago by 41k • written 9.6 years ago by ★ 1.8k
10
votes
4
replies
10k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 8 months ago by 41k • written 4.4 years ago by 5.7k
10
votes
31
replies
9.9k
views
10 follow
Tutorial: OrthoMCL installation on Ubuntu Linux
ubuntu orthomcl mysql linux
updated 5 weeks ago by • 0 • written 5.9 years ago by ▴ 320
11
votes
7
replies
9.8k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 6 months ago by 41k • written 2.7 years ago by ▴ 360
18
votes
2
replies
9.8k
views
Tutorial: Video: RNA-Seq Alignment and Visualization using Galaxy and IGB
RNA-Seq Galaxy IGB
updated 20 months ago by 41k • written 9.1 years ago by ▴ 860
14
votes
0
replies
9.3k
views
Tutorial: How to generate PCA plot and heatmaps in R
heatmap PCA RNA-Seq R
updated 7 months ago by 41k • written 7.2 years ago by ★ 3.6k
48
votes
30
replies
9.3k
views
11 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
updated 28 days ago by 78k • written 7.7 years ago by 41k
61
votes
6
replies
9.3k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 9 months ago by 41k • written 10.3 years ago by 9.7k
16
votes
5
replies
8.8k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 9 months ago by 41k • written 11.2 years ago by 20k
19
votes
4
replies
8.7k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 9 months ago by 41k • written 10.7 years ago by 99k
20
votes
0
replies
8.6k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 9 months ago by 41k • written 11.2 years ago by 99k
10
votes
1
reply
8.6k
views
Tutorial: How to select reads with specific flag using samtools
next-gen-sequencing
updated 6 months ago by 41k • written 6.2 years ago by ▴ 110
25
votes
15
replies
8.6k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 9 months ago by 41k • written 10.9 years ago by 9.7k
9
votes
0
replies
8.5k
views
Tutorial: Installing And Running Ncbi Blast
blast
updated 9 months ago by 41k • written 11.6 years ago by ▴ 540
3
votes
2
replies
8.4k
views
Tutorial: Use fastp to preprocess FASTQ data with unique molecular identifer (UMI) integrated
FASTQ UMI fastp
updated 6 months ago by 41k • written 6.0 years ago by ★ 2.5k
20
votes
4
replies
8.4k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 7 months ago by 41k • written 7.2 years ago by ★ 4.2k
383 results • Page 2 of 8
Recent Votes
Comment: unicycler error : [Errno 13] Permission denied:
Comment: unicycler error : [Errno 13] Permission denied:
Answer: SPAdes error: finished abnormally, OS return value: 21
Comment: SPAdes error: finished abnormally, OS return value: 21
Removing UMI with UMI tools?
Extract UMIs using UMI-tools
Answer: Good alignment rate for DNA-seq data
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Popular Question to O.rka ▴ 710
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Recent Replies
Comment: frequency plot for peaks by Ankit ▴ 400
what is your txdb? can you explain your experiment in detail?
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by cmdcolin ★ 3.4k
paste the file in csv format and a R wizard might come along and help :)
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when by rpolicastro 12k
Your intuition was correct. You want to make two separate data frames and join them on sample name. This code is untested but will probably…
Comment: Generate Read counts from bam file by ATpoint 78k
It has nothing to do with low complexity. You always map to the entire genome since the reads can come from the entire genome. If you take …
Comment: CHIPSEQ : Cut AND Run , DiffBind Parameters by ATpoint 78k
DiffBind uses DESeq2 for differential analysis and its method to moderate logFCs. When noise is high and there is little evidence for diffe…
Comment: p-value combination methods by dsull ★ 5.0k
Was this response written by a LLM? It's a useful response but it doesn't really answer the initial question... In response to the OP ques…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by RNAseqer ▴ 250
Well, because I want to also draw attention to nominally significant genes as they are subjected to follow up experiments and would be nice…
Comment: Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not pres by Nitin Narwade ★ 1.5k
Actually, to add an **EXACT line/mark** for one value based on another is impossible (for me at least). What you can do is, select the min…
Comment: Construction of single sequence assembly out of contigs by analyst ▴ 10
Thanks colindaven!
Comment: Generate Read counts from bam file by Enrique • 0
Great appreciation. If you don't use restrictive arguments in the mapping, is better to use the entire genome to avoid the false positives …
Comment: Generate Read counts from bam file by ATpoint 78k
No, absolutely not. Mapping to such a tiny subset leads to false positives. Use the entire genome that includes the mt reference.
Answer: Generate Read counts from bam file by Enrique • 0
Hello, I recommend you using the mitochondrial reference genome. For the GTF file (or GFF, they are in general the same), checkout this pos…
Comment: How to deeply sequence long inserts by Brian Bushnell 19k
Merging paired reads is a good idea. Then you get nice, long reads... and actually, as long as you have enough coverage, you can just mer…
Answer: bam or VCF files from GSE75010 by ATpoint 78k
It's a gene expression **array**, not RNA-seq. Arrays do not allow variant calling as there is no digital sequencing data created.
Answer: Generate Read counts from bam file by ATpoint 78k
I don't follow. You always align to the full genome (which includes the mt genome in case of human reference genomes). Anyway, if you g…
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