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346 results • Page 2 of 7
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4
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2
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1.9k
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Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle 5.0 Tutorial
updated 18 months ago by 123k • written 3.5 years ago by ★ 9.2k
43
votes
14
replies
48k
views
10 follow
Tutorial: Using R in Conda
R Tutorial
updated 4 weeks ago by ▴ 20 • written 2.4 years ago by ▴ 680
31
votes
9
replies
20k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda Tutorial
updated 6 months ago by • 0 • written 2.3 years ago by ▴ 140
98
votes
16
replies
29k
views
18 follow
Tutorial: Heatmaps in R
Tutorial R heatmap
7 months ago by Jean-Karim Heriche 26k
21
votes
2
replies
3.0k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 12 weeks ago by ▴ 40 • written 19 months ago by 7.4k
31
votes
6
replies
7.6k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
complexheatmap clustering arthritis pam Tutorial
15 months ago by Kevin Blighe 83k
78
votes
41
replies
27k
views
24 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 11 days ago by • 0 • written 9.1 years ago by ★ 7.6k
8
votes
0
replies
1.9k
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
20 months ago by rpolicastro 10k
234
votes
176
replies
82k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 6 weeks ago by 37k • written 7.3 years ago by ★ 4.6k
6
votes
0
replies
1.2k
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
20 months ago by rpolicastro 10k
8
votes
1
reply
896
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk fasta Tutorial
20 months ago by Kevin Blighe 83k
15
votes
9
replies
3.9k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R tidyverse gene Tutorial
updated 14 months ago by ★ 1.1k • written 2.3 years ago by 10k
12
votes
2
replies
949
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R Tutorial
20 months ago by rpolicastro 10k
146
votes
35
replies
57k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics Tutorial next-gen
updated 7 months ago by • 0 • written 10.0 years ago by ★ 1.6k
14
votes
2
replies
2.5k
views
Tutorial: Methylation Analysis Tutorial in R_part2
RNA-Seq R methylation Tutorial cancer
3 months ago by Hamid Ghaedi 2.7k
4
votes
0
replies
1.5k
views
Tutorial: Building mosdepth on macOS
mosdepth nim Tutorial
20 months ago by ATpoint 66k
16
votes
7
replies
11k
views
Tutorial: Integrating VDJ sequencing data with Seurat
Seurat clonotyping VDJ sc-RNAseq Tutorial
updated 21 months ago by 8.6k • written 3.5 years ago by ▴ 310
273
votes
33
replies
88k
views
24 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 10 months ago by ▴ 100 • written 9.1 years ago by 20k
5
votes
0
replies
3.2k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap Tutorial
22 months ago by GenoMax 123k
10
votes
0
replies
3.9k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap Tutorial
22 months ago by GenoMax 123k
10
votes
0
replies
2.3k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap Tutorial
22 months ago by GenoMax 123k
11
votes
1
reply
2.0k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq Tutorial
updated 12 months ago by 66k • written 23 months ago by ★ 21k
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell Tutorial flow-cytometry
10 days ago by Ahill ★ 1.9k
0
votes
1
reply
2.2k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
taxonomy python biosql Tutorial
updated 24 months ago by • 0 • written 4.3 years ago by ▴ 310
76
votes
13
replies
14k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 13 months ago by 37k • written 8.5 years ago by 19k
6
votes
10
replies
4.1k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
dna methylation Tutorial DMR
24 months ago by dec986 ▴ 340
41
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
maf vcf ensembl tcga somatic Tutorial
24 months ago by Cyriac Kandoth 5.8k
5
votes
2
replies
4.2k
views
Tutorial: bam2rpkm by bedtools
RNA-Seq bam rpkm bedtools Tutorial
updated 2.0 years ago by 66k • written 5.1 years ago by ▴ 130
16
votes
11
replies
7.2k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation Tutorial
3 months ago by Ram 37k
42
votes
33
replies
6.4k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation Tutorial
2.0 years ago by Ram 37k
95
votes
6
replies
21k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
snakemake conda workflow Tutorial
updated 2.1 years ago by ▴ 50 • written 4.3 years ago by 15k
17
votes
40
replies
15k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
run easy orthomcl all-v-all mcl Tutorial
updated 2.1 years ago by ★ 2.0k • written 6.4 years ago by ▴ 160
23
votes
4
replies
5.8k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
enrichedheatmap chip-seq atac-seq heatmap Tutorial
updated 17 months ago by ★ 1.2k • written 3.3 years ago by 66k
13
votes
4
replies
3.9k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
R RNA-Seq Transcriptomics Tutorial bioconductor
10 months ago by Thind amarinder ▴ 280
26
votes
0
replies
2.0k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
variant interpretation annotation clinical cancer Tutorial
2.2 years ago by Malachi Griffith 19k
10
votes
1
reply
1.9k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
COVID-19 fastv Tutorial SARS-CoV-2
2.2 years ago by chen ★ 2.4k
60
votes
49
replies
38k
views
22 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 19 months ago by 37k • written 6.2 years ago by ★ 3.3k
10
votes
7
replies
4.1k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
STAR STARsolo 10x Chromium Tutorial
updated 11 months ago by 123k • written 2.2 years ago by 83k
17
votes
17
replies
6.1k
views
9 follow
Tutorial: Create de novo repeat library
Tutorial repeat annotation de-novo
updated 15 months ago by • 0 • written 3.0 years ago by 7.4k
0
votes
0
replies
761
views
Tutorial: BrainArray CDF, annotation, etc
brainarray cdf db Tutorial
2.2 years ago by Kevin Blighe 83k
38
votes
0
replies
5.3k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
RNA-Seq batch correction edgeR ma-plot Tutorial
2.2 years ago by ATpoint 66k
12
votes
0
replies
1.9k
views
Tutorial: Long versus wide data for plotting genomics data in R.
R tidyverse ggplot2 Tutorial data.table
20 months ago by rpolicastro 10k
75
votes
70
replies
15k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment Tutorial david
updated 10 months ago by • 0 • written 4.8 years ago by 83k
1
vote
1
reply
976
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed txt bed2txt sequencing Tutorial
2.3 years ago by opheevallee • 0
4
votes
3
replies
3.7k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy tool R Tutorial
updated 18 months ago by ▴ 240 • written 4.7 years ago by ★ 3.9k
4
votes
1
reply
944
views
Tutorial: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED BEDtools Tutorial Video Lesson
2.3 years ago by sdsubaru33 ▴ 40
3
votes
0
replies
2.4k
views
Tutorial: Sorting GFF/GTF files
annotation gff gtf sort Forum Tutorial
2.4 years ago by Juke34 7.4k
20
votes
6
replies
4.6k
views
Tutorial: Open Targets and programmatic access
drug API bioinformatics open targets disease Tutorial
2.4 years ago by Denise CS ★ 5.2k
2
votes
2
replies
1.3k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
SNP snpEff Annotation Tutorial chrMT
2.4 years ago by Arup Ghosh 3.1k
10
votes
3
replies
1.5k
views
Tutorial: FASTA file split
Tutorial split fasta tutorial
5 months ago by Juke34 7.4k
346 results • Page 2 of 7
Recent Votes
A: How to get Go Terms IDs from given a file that contains gene Ensembl IDs with a
Comment: How to calculate the offset for a riboseq experiment
Treating "patient" as a batch effect
How to calculate the offset for a riboseq experiment
Answer: Running nf-core rnaseq with smart-seq3 data
Answer: How can I use nohup command when filtering SNPs?
Answer: How to calculate the offset for a riboseq experiment
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Teacher to ATpoint 66k
Scholar to Jack Tierney ▴ 20
Popular Question to langziv ▴ 20
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Popular Question to Assa Yeroslaviz ★ 1.7k
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Recent Replies
Answer: VEP annotated vcf is not readable in bcftools by barslmn • 0
Bcftools can read and [parse][1] VEP annotated vcf files. You can then format the output as you like. Are you using "--vcf" option when r…
Comment: Add artificial intelligence training related disclaimers to your profile by JC 13k
Maybe a site-wide licensing could be better? I think the website contains a lot of knowledge from a diverse group, some members are no long…
Comment: molecular docking by Matthias Zepper 2.3k
I somehow feel your professor is asking a bit too much from you to just provide you with the files but no prior lessons. We had at least a …
Comment: How to calculate the offset for a riboseq experiment by Jack Tierney ▴ 20
ORFik and Shoelaces both emanate from Valen group in Bergen. Lots of tools handle these ideas however their figure was just the first to co…
Comment: Create a nested dictionary from a text file by Joe 20k
Is there a particular reason you need it in a nested dictionary? I think you are probably making your life unnecessarily hard by trying to …
Comment: Splitting CRAM files by langziv ▴ 20
Thanks. So it means that it's a single genome?
Comment: STAR error with a loop by luzglongoria ▴ 40
If I do ls *.fp.fq.gz | sed 's/_[12].fp.fq.gz//' | sort | uniq | while read F; do echo "run with ${F}_1.fq.gz and ${F}_2.fq.gz " ; do…
Comment: VEP annotated VCF conversion into TSV/Text by yussab ▴ 80
Hi Nai, I suggest you to get the installation done with conda and try this script, it'll save you a look of time ;) I've already tried most…
Comment: Box plots with logFC values by myfam128 • 0
Thank you I will try that
Comment: Box plots with logFC values by myfam128 • 0
I am trying to show If a gene is up-regulated or down-regulated
Answer: How to remove duplicate rows by averaging their values having 1 million rows X 1 by Gordon Smyth ★ 5.2k
The `avereps()` function of the limma package does exactly that. In R of course rather than Excel. But see https://support.bioconductor.or…
Comment: minimap2, before or after assembly? by samuel.a.odonnell ▴ 430
It entirely depends what you want to do.
Comment: How to calculate the offset for a riboseq experiment by Assa Yeroslaviz ★ 1.7k
Thanks I know of `ORFik`, as I have used it for a different analysis, but I'll also take a look at `showlaces`, for the sake of completenes…
Comment: How can I use nohup command when filtering SNPs? by Joe 20k
Define 'not working'? Pierre's suggestion is the better option, but have you looked at the log file? When you run a process with nohup and…
Comment: VEP annotated VCF conversion into TSV/Text by Nai ▴ 20
Should I apply into this: bcftools +split-vep test/split-vep.vcf -f -duplicate '%CHROM:%POS %CSQ\n' -d -A tab
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