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232 results • Page 2 of 5
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42
votes
19
replies
7.1k
views
8 follow
Tutorial: Designing Command-Line Interfaces (Clis) For Scientific Software
software
updated 4 weeks ago by 38k • written 10.1 years ago by 4.1k
42
votes
2
replies
17k
views
Tutorial: Sequencing Technology Review Papers
sequencing papers
updated 4 weeks ago by 38k • written 10.6 years ago by 97k
42
votes
16
replies
21k
views
15 follow
Tutorial: Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC varscan2 CNV copy-number
updated 7 months ago by 38k • written 7.5 years ago by ★ 2.3k
42
votes
33
replies
6.8k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation
12 days ago by Ram 38k
40
votes
9
replies
10k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 20 days ago by 38k • written 9.0 years ago by ★ 1.9k
37
votes
8
replies
9.2k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 17 days ago by 38k • written 2.5 years ago by 2.9k
34
votes
15
replies
18k
views
12 follow
Tutorial: TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen GDC R TCGA
updated 11 days ago by 38k • written 6.5 years ago by ▴ 310
34
votes
15
replies
5.0k
views
6 follow
Tutorial: How to do data cleaning for VCF genetic file
vcf
updated 12 days ago by 38k • written 3.8 years ago by ★ 9.3k
34
votes
4
replies
5.5k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 4 months ago by 38k • written 7.7 years ago by ▴ 370
33
votes
16
replies
15k
views
10 follow
Tutorial: Machine Learning For Cancer Classification - Part 3 - Predicting With A Random Forest Classifier
machine-learning classification
updated 25 days ago by 38k • written 9.3 years ago by 20k
32
votes
4
replies
6.4k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 9 days ago by 38k • written 4.4 years ago by ★ 1.5k
31
votes
9
replies
24k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 12 days ago by 38k • written 2.6 years ago by ▴ 140
31
votes
6
replies
8.7k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 12 days ago by 38k • written 2.8 years ago by 84k
31
votes
12
replies
26k
views
7 follow
Tutorial: So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control fastqc
updated 26 days ago by 38k • written 9.4 years ago by 97k
30
votes
6
replies
21k
views
Tutorial: Transforming And Manipulating Color Space Reads
conversion solid
updated 6 months ago by 38k • written 10.9 years ago by 97k
30
votes
14
replies
15k
views
8 follow
Tutorial: Installation of the MuSiC suite on unsupported Linux distributions
genome-music linux smg
updated 4 weeks ago by 38k • written 10.1 years ago by 5.9k
30
votes
8
replies
10k
views
7 follow
Tutorial: How To Create A Bioinformatics Pipeline Using Spotify !
python pipeline
updated 20 days ago by 38k • written 9.0 years ago by ▴ 800
29
votes
5
replies
5.9k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 26 days ago by 38k • written 9.5 years ago by ★ 4.3k
28
votes
4
replies
3.7k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 11 days ago by 38k • written 4.2 years ago by 26k
27
votes
0
replies
2.7k
views
Tutorial: Building Docker images
singularity docker container
8 months ago by ATpoint 70k
26
votes
10
replies
58k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 17 days ago by 38k • written 2.0 years ago by ★ 1.3k
26
votes
17
replies
6.7k
views
8 follow
Tutorial: virtualenv - running Python based software in isolation
python virtualenv
updated 6 months ago by 38k • written 8.6 years ago by 5.9k
26
votes
0
replies
2.1k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 12 days ago by 38k • written 3.4 years ago by 19k
24
votes
15
replies
7.9k
views
8 follow
Tutorial: Syllabus To Learn Bioinformatics From Online Video Resources
course training mooc
updated 4 weeks ago by 38k • written 10.2 years ago by 9.5k
23
votes
4
replies
6.2k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 12 days ago by 38k • written 3.6 years ago by 70k
22
votes
1
reply
3.0k
views
Tutorial: Introduction To R Course Materials Available
R
updated 11 weeks ago by 38k • written 10.9 years ago by 26k
21
votes
2
replies
3.7k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 6 months ago by ▴ 40 • written 23 months ago by 7.7k
20
votes
4
replies
2.2k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 12 days ago by 38k • written 3.9 years ago by ▴ 180
20
votes
0
replies
8.4k
views
Tutorial: Metagenomics Review Papers
metagenomics papers
updated 4 weeks ago by 38k • written 10.6 years ago by 97k
20
votes
6
replies
4.8k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 12 days ago by 38k • written 6.5 years ago by ★ 5.2k
20
votes
7
replies
5.6k
views
Tutorial: Showing up and down regulated GO and pathway using enrichR and ggplot2
ggplot2 RNA-Seq R
updated 12 days ago by 38k • written 4.4 years ago by ▴ 740
20
votes
4
replies
13k
views
Tutorial: How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor affymetrix
updated 4 weeks ago by 38k • written 10.0 years ago by 20k
20
votes
10
replies
4.6k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 12 days ago by 38k • written 2.6 years ago by 11k
19
votes
4
replies
8.4k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 4 weeks ago by 38k • written 10.1 years ago by 97k
19
votes
9
replies
6.0k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 27 days ago by 38k • written 9.8 years ago by 9.5k
18
votes
22
replies
7.1k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 12 days ago by 38k • written 3.3 years ago by 7.7k
17
votes
3
replies
11k
views
Tutorial: bedGraphToBigWig Tutorial and Report
bedGraphToBigWig
updated 8 months ago by 38k • written 7.1 years ago by ★ 9.3k
17
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 12 days ago by 38k • written 6.7 years ago by ▴ 160
16
votes
11
replies
7.3k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
12 days ago by Ram 38k
16
votes
7
replies
12k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 12 days ago by 38k • written 3.8 years ago by ▴ 310
16
votes
0
replies
12k
views
Tutorial: Workshop - Analysis Of Next Generation Sequencing Data
RNA-seq
updated 4 weeks ago by 38k • written 11.0 years ago by 9.9k
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 12 days ago by 38k • written 6.4 years ago by ★ 4.6k
16
votes
5
replies
8.4k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 4 weeks ago by 38k • written 10.5 years ago by 20k
15
votes
2
replies
2.7k
views
Tutorial: Introduction to bedtools.
bedtools
updated 17 days ago by 38k • written 8.4 years ago by 11k
15
votes
4
replies
4.1k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 12 days ago by 38k • written 2.7 years ago by ▴ 300
15
votes
0
replies
6.3k
views
Tutorial: Introduction To Ngs Bioinformatics By The Bioinformatics Team At The University Of Texas
course training
updated 4 weeks ago by 38k • written 10.8 years ago by 97k
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 17 days ago by 38k • written 5.3 years ago by ▴ 740
15
votes
2
replies
1.4k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 5 months ago by ▴ 810 • written 18 months ago by ▴ 270
15
votes
2
replies
6.5k
views
Tutorial: Genotype And Snp Calling Review Papers
snp
updated 4 weeks ago by 38k • written 10.6 years ago by 97k
14
votes
2
replies
6.1k
views
Tutorial: ChIP-seq analysis tutorial
Tutorials ChIP-Seq
updated 6 months ago by 38k • written 7.6 years ago by ★ 2.9k
232 results • Page 2 of 5
Recent Votes
A: circos plot gene expression by RNA-Seq
Create Interval List for Picard CollectRNASeqmetrics
Answer: multiallelic variants
Answer: LIMMA calculates identical adj.P.Val for different proteins from proteomics
Comment: Hard clip fastq
Answer: Hard clip fastq
Answer: Hard clip fastq
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Popular Question to Lluís R. ★ 1.2k
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Recent Replies
Answer: Installing rlang version 1.1.0 by Lluís R. ★ 1.2k
Having a package duplicated means they are at a different `.libPaths()` sites. Check which version is in which directory and directly remov…
Answer: Somatic truth set by samuel ▴ 180
I think I have found an naswer to my own question. Should anyone have the same question as of March 2023 the relevant data and information…
Answer: GetBM - GERP conservation score for GRCm39 by Kyle • 0
Final solution thanks to Ben's help:: # convert df to Grange. snp_gr <-makeGRangesFromDataFrame(BM_SNPs, seqnames.field = "seqnam…
Comment: GetBM - GERP conservation score for GRCm39 by Kyle • 0
Perfect answer, thanks Ben!
Answer: MapSplice2 gives error if the thread count (-p value) is greater than 2 by vishal.koparde ▴ 10
Any updates??
Comment: how to know what adapter sequences to trim for RNA-seq? by lunarskye222 • 0
Do you happen to know if the middle part of this udi barcode (GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTACATATCTCG) is also part of the TruSeq a…
Comment: Hard clip fastq by GenoMax 127k
If you simply want the reads to be compatible in length then do not adapter trim.
Comment: Hard clip fastq by samuel ▴ 180
@ATpoint, so no adapter trimming first? Just trim the raw fastq?
Answer: Confused on strandedness, what are antisense transcripts? by dsull ★ 4.0k
Think of it on the DNA level: If the mRNA made is the same sequence as the "sense" DNA strand (except U's instead of T's), it is a "sense" …
Comment: Protein name in GenBank by GenoMax 127k
If you must do this programmatically then collect all cases where things differ in order of words (or number of words) like the example abo…
Answer: Hard clip fastq by GenoMax 127k
You can also use `reformat.sh` from [**BBMap suite**][1] as follows reformat.sh -Xmx2g in1=R1.fq.gz in2=R2.fq.gz out1=R1_trim.fq.gz …
Answer: Hard clip fastq by ATpoint 70k
Use `seqtk trimfq`. It makes sense to trim first to your desired length and then run identical downstream processing for a fair comparison.…
Comment: Protein name in GenBank by Mensur Dlakic ★ 23k
I think you either take time to do it properly, or you will end up missing some proteins. BLAST sequence search, even on 1500 genomes, can …
Comment: Log2 FC Threshold by ATpoint 70k
Since OP is using GEO2R which uses limma the appropriate function (need to run manually, GEO2R does not support) is `limma::treat()` rather…
Answer: Adding median value to VlnPlot in Seurat by Ming Tommy Tang ★ 2.9k
If you know ggplot2, you can `get_expression_data` function in here https://divingintogeneticsandgenomics.rbind.io/post/how-to-do-gene-corr…
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