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349 results • Page 2 of 7
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12
votes
2
replies
829
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R Tutorial
15 months ago by rpolicastro 8.9k
147
votes
35
replies
55k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics Tutorial next-gen
updated 8 weeks ago by • 0 • written 9.6 years ago by ★ 1.6k
14
votes
2
replies
2.1k
views
Tutorial: Methylation Analysis Tutorial in R_part2
methylation RNA-Seq R cancer Tutorial
16 months ago by Hamid Ghaedi ★ 2.5k
4
votes
0
replies
1.4k
views
Tutorial: Building mosdepth on macOS
mosdepth nim Tutorial
15 months ago by ATpoint 62k
7
votes
6
replies
2.6k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
Software clusterProfiler Tool rna-seq tool
updated 10 months ago by 21k • written 16 months ago by ▴ 160
76
votes
32
replies
13k
views
17 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
R pathway enrichment active subnetwork Tutorial
updated 16 months ago by ▴ 30 • written 4.0 years ago by ★ 1.2k
15
votes
7
replies
9.7k
views
Tutorial: Integrating VDJ sequencing data with Seurat
Seurat clonotyping VDJ sc-RNAseq Tutorial
updated 16 months ago by 8.4k • written 3.1 years ago by ▴ 300
265
votes
33
replies
83k
views
24 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 5 months ago by ▴ 100 • written 8.7 years ago by 19k
5
votes
0
replies
2.8k
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
17 months ago by GenoMax 117k
8
votes
0
replies
3.1k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap Tutorial
17 months ago by GenoMax 117k
9
votes
0
replies
1.8k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap Tutorial
17 months ago by GenoMax 117k
11
votes
1
reply
1.7k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq Tutorial
updated 7 months ago by 62k • written 18 months ago by ★ 20k
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell Tutorial flow-cytometry
7 months ago by Ahill ★ 1.9k
0
votes
1
reply
2.1k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
taxonomy python biosql Tutorial
updated 19 months ago by • 0 • written 3.9 years ago by ▴ 310
76
votes
13
replies
13k
views
12 follow
Tutorial: Exploring cancer mutation data portals
TCGA Cancer ICGC Data-Portal Mutation
updated 8 months ago by 36k • written 8.1 years ago by 19k
6
votes
10
replies
3.8k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
dna methylation Tutorial DMR
19 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
19 months ago by Cyriac Kandoth 5.8k
5
votes
2
replies
3.8k
views
Tutorial: bam2rpkm by bedtools
RNA-Seq bam rpkm bedtools Tutorial
updated 19 months ago by 62k • written 4.7 years ago by ▴ 130
16
votes
11
replies
6.9k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation Tutorial
19 months ago by Ram 36k
41
votes
33
replies
6.1k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation Tutorial
19 months ago by Ram 36k
93
votes
6
replies
19k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
snakemake conda workflow Tutorial
updated 20 months ago by ▴ 30 • written 3.8 years ago by 15k
17
votes
40
replies
14k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
run easy orthomcl all-v-all mcl Tutorial
updated 20 months ago by ★ 1.9k • written 6.0 years ago by ▴ 160
23
votes
4
replies
5.3k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
enrichedheatmap chip-seq atac-seq heatmap Tutorial
updated 12 months ago by ★ 1.1k • written 2.9 years ago by 62k
13
votes
4
replies
3.7k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
R RNA-Seq Transcriptomics Tutorial bioconductor
5 months ago by Thind amarinder ▴ 260
26
votes
0
replies
1.8k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
variant interpretation annotation clinical cancer Tutorial
21 months ago by Malachi Griffith 19k
10
votes
1
reply
1.8k
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
21 months ago by chen ★ 2.4k
60
votes
49
replies
36k
views
22 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 13 months ago by 36k • written 5.8 years ago by ★ 3.2k
10
votes
7
replies
3.4k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
STAR STARsolo 10x Chromium Tutorial
updated 6 months ago by 117k • written 21 months ago by 82k
15
votes
17
replies
5.3k
views
9 follow
Tutorial: Create de novo repeat library
Tutorial repeat annotation de-novo
updated 10 months ago by • 0 • written 2.6 years ago by ★ 7.1k
0
votes
0
replies
643
views
Tutorial: BrainArray CDF, annotation, etc
brainarray cdf db Tutorial
21 months ago by Kevin Blighe 82k
37
votes
0
replies
4.6k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
RNA-Seq batch correction edgeR ma-plot Tutorial
22 months ago by ATpoint 62k
10
votes
0
replies
1.6k
views
Tutorial: Long versus wide data for plotting genomics data in R.
R tidyverse ggplot2 Tutorial data.table
15 months ago by rpolicastro 8.9k
75
votes
70
replies
14k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment Tutorial david
updated 5 months ago by • 0 • written 4.4 years ago by 82k
1
vote
1
reply
841
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed txt bed2txt sequencing Tutorial
23 months ago by opheevallee • 0
4
votes
3
replies
3.5k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy tool R Tutorial
updated 13 months ago by ▴ 210 • written 4.2 years ago by ★ 3.9k
4
votes
1
reply
810
views
Tutorial: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED BEDtools Tutorial Video Lesson
23 months ago by sdsubaru33 ▴ 40
72
votes
59
replies
20k
views
15 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000 genomes PCA VCF PLINK Tutorial
updated 9 months ago by • 0 • written 4.8 years ago by 82k
3
votes
0
replies
2.0k
views
Tutorial: Sorting GFF/GTF files
annotation gff gtf sort Forum Tutorial
23 months ago by Juke34 ★ 7.1k
20
votes
6
replies
4.4k
views
Tutorial: Open Targets and programmatic access
drug API bioinformatics open targets disease Tutorial
24 months ago by Denise CS ★ 5.2k
2
votes
2
replies
1.1k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
SNP snpEff Annotation Tutorial chrMT
2.0 years ago by Arup Ghosh 2.9k
10
votes
3
replies
1.2k
views
Tutorial: FASTA file split
Tutorial split fasta tutorial
20 days ago by Juke34 ★ 7.1k
0
votes
0
replies
837
views
Tutorial: VIDEO: Installing BLAST Databases on Your Own Computer
sequence BLAST databases Linux MacOSX Tutorial
2.1 years ago by brian.fristensky ▴ 270
0
votes
0
replies
618
views
Tutorial: VIDEO: BLAST Searches Through a Data Science Lens
sequence BLAST Data Science Covid19 Tutorial
2.1 years ago by brian.fristensky ▴ 270
2
votes
1
reply
954
views
Tutorial: A very simple way to detect viruses and microorganisms from mNGS FASTQ data using fastv
SARS-CoV-2 COVID-19 viruses fastv Tutorial
2.1 years ago by chen ★ 2.4k
63
votes
25
replies
22k
views
14 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
rna-seq tutorial Tutorial
updated 2.1 years ago by 36k • written 8.4 years ago by 93k
55
votes
41
replies
17k
views
16 follow
Tutorial: Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
arrow pbalign pacbio polishing smrt limk Tutorial
updated 2.2 years ago by • 0 • written 4.8 years ago by ★ 1.4k
20
votes
7
replies
5.1k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
RNA-Seq R ggplot2 Tutorial
2.2 years ago by ahmad mousavi ▴ 690
4
votes
0
replies
1.1k
views
Tutorial: NIH CDE browser for TCGA clinical data CDE codes
tcga nih cde metadata Tutorial
2.2 years ago by Kevin Blighe 82k
11
votes
26
replies
3.2k
views
Tutorial: gene set filter/selection for training ab initio annotation tools
genome gene Tutorial
updated 11 months ago by ▴ 610 • written 2.9 years ago by ★ 7.1k
11
votes
1
reply
4.2k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
RNA-Seq scRNA-seq CITE-seq-count Tutorial
2.3 years ago by colindaven ★ 3.9k
349 results • Page 2 of 7
Recent Votes
Comment: Multiple exposure timelines (time-points) in one DESeq2 object or multiple DESeq
Comment: Multiple exposure timelines (time-points) in one DESeq2 object or multiple DESeq
Answer: Convert a BAM from GRCh37 to hg19?
Comment: Convert a BAM from GRCh37 to hg19?
Answer: Multiple exposure timelines (time-points) in one DESeq2 object or multiple DESeq
A: Need help choosing genes and calculating ranks for GSEA rank file
Need help choosing genes and calculating ranks for GSEA rank file
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Recent Replies
Answer: How to subset a GVCF using GATK SelectVariants by Pierre Lindenbaum 146k
https://gatk.broadinstitute.org/hc/en-us/articles/360037055952-SelectVariants#--sample-name > --sample-name / -sn > This argument c…
Comment: How to subset a GVCF using GATK SelectVariants by Pierre Lindenbaum 146k
are you sure it's safe reduce the number of samples from a g.vcf file (!= vcf) ?
Comment: Multiple exposure timelines (time-points) in one DESeq2 object or multiple DESeq by Rafael Soler ▴ 430
Oh, I see. Thank you :)
Comment: Convert a BAM from GRCh37 to hg19? by Giovanni M Dall'Olio 27k
Thanks for sharing the solution!
Comment: Statistical test for RNAseq Clustering by HERMAN • 0
Thank you very much for your reply ! I will try to discuss this with my biologist colleagues
Comment: Multiple exposure timelines (time-points) in one DESeq2 object or multiple DESeq by ATpoint 62k
+1, fyi you can simply post a plain biostars link to an existing thread/answer, it will then display the title of the thread, there is no n…
Comment: Convert a BAM from GRCh37 to hg19? by GenoMax 117k
While major genome builds are identical there are specific differences in non-chromosomal members: https://gatk.broadinstitute.org/hc/en-us…
Answer: Convert a BAM from GRCh37 to hg19? by Joel Wallenius ▴ 100
I ended up using samtools reheader, as the chromosomes seemed similar enough. I ended up wasting some hours thinking reheader ONLY changed …
Comment: PLINK CASE-CONTROL ANALYSIS by Nai ▴ 20
Dear Pierre, Sorry, I would like to perform in Plink. The question is to generate .bed, .map. .fim files from csv files having Marker, var…
Answer: gene library composition by Rafael Soler ▴ 430
Hello! You can put these genes in websites like [DAVID][1], [REACTOME][2], or [PANTHER][3] to classify them according to their functions…
Comment: Validate mutations from WGS using RNA-seq bam files in IGV? by Arup Ghosh 2.9k
The authors have mentioned using two approaches for validation. Although they have not mentioned the exact criteria for the RNA-seq based a…
Answer: Multiple exposure timelines (time-points) in one DESeq2 object or multiple DESeq by Rafael Soler ▴ 430
The dispersion estimates will change depending on whether you analyze the data together or separately, so the best strategy depends on the …
Answer: Extract all regions in a genome that are not assembly gaps from a FASTA file qui by Ivan ▴ 50
What Pierre Lindenbaum posted works, but I couldn't be bothered to install another software to my space. The stuff I wrote in Python was v…
Comment: Overlapping regions in a BED file by GenoMax 117k
They are standard feature types (describing gene and its products) that are defined in GTF/GFF files from which your BED file is likely der…
Answer: Hands-On RNA-Seq Data Analysis Workshop in Leipzig, Germany (October 25-28, 2022 by David Langenberger 9.7k
**Update**: If there are limitations on the number of participants due to rising Covid 19 cases, priority will be given to those who have r…
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