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323 results • Page 2 of 7
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Tutorial: ViennaRNA package installation in Windows
windows rna mfold viennarna
updated 3 months ago by 40k • written 12 months ago by ▴ 20
132
votes
123
replies
33k
views
23 follow
Tutorial: Survival analysis with gene expression
cox gene-expression survival-analysis geo
updated 6 months ago by ★ 1.1k • written 5.0 years ago by 86k
11
votes
7
replies
9.2k
views
Tutorial: ClusterProfiler A software for functional enrichment of differentially expressed genes- A tutorial
clusterProfiler Software rna-seq
updated 4 months ago by 40k • written 2.6 years ago by ▴ 360
84
votes
21
replies
19k
views
16 follow
Tutorial: Gene Set Enrichment Analysis
microarray enrichment RNA-Seq GSEA
updated 6 months ago by 40k • written 3.0 years ago by 3.0k
83
votes
34
replies
17k
views
22 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment R pathway active-subnetwork
updated 4 months ago by • 0 • written 5.3 years ago by ★ 1.3k
85
votes
2
replies
56k
views
6 follow
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 7 months ago by 40k • written 10.3 years ago by 11k
15
votes
5
replies
12k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 6 months ago by 40k • written 5.8 years ago by ▴ 760
39
votes
8
replies
11k
views
10 follow
Tutorial: Methylation Analysis Tutorial in R_part1
cancer R methylation
updated 6 months ago by 40k • written 3.0 years ago by 3.0k
7
votes
14
replies
3.0k
views
6 follow
Tutorial: Install required dependencies for GATK4 on remote server without root privilege
gatk
updated 11 months ago by • 0 • written 19 months ago by ▴ 30
75
votes
14
replies
15k
views
15 follow
Tutorial: List Of Bioinformatics Books
books
updated 7 months ago by 40k • written 10.4 years ago by 9.7k
4
votes
13
replies
11k
views
Tutorial: Merging multiple vcf files into Single vcf file
vcf bcftools
updated 3 months ago by 40k • written 4.6 years ago by ▴ 140
12
votes
4
replies
5.0k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 7 months ago by 40k • written 2.6 years ago by ▴ 130
27
votes
10
replies
70k
views
9 follow
Tutorial: Installing an updated R version (>=4.0) using conda
software-error R
updated 6 months ago by 40k • written 2.5 years ago by ★ 1.4k
146
votes
70
replies
46k
views
20 follow
Tutorial: Network plot from expression data in R using igraph
microarray RNA-Seq R network
updated 4 weeks ago by ▴ 260 • written 5.9 years ago by 86k
15
votes
2
replies
1.8k
views
Tutorial: Germline variant calling pipeline using Snakemake
snakemake GATK germline_variant_calling
updated 11 months ago by ▴ 810 • written 2.0 years ago by ▴ 280
196
votes
44
replies
70k
views
33 follow
Tutorial: Analysing Microarray Data In Bioconductor
microarray-analysis bioconductor
updated 8 months ago by 40k • written 11.0 years ago by 20k
45
votes
2
replies
36k
views
Tutorial: Mapping Reads With Bwa And Bowtie
bowtie bwa
updated 7 months ago by 40k • written 11.5 years ago by ▴ 540
93
votes
105
replies
39k
views
25 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes PLINK PCA
updated 6 months ago by 40k • written 5.1 years ago by 86k
116
votes
66
replies
43k
views
20 follow
Tutorial: [Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera fastq-dump Fastq ENA
updated 6 months ago by 40k • written 5.2 years ago by 77k
65
votes
26
replies
13k
views
11 follow
Tutorial: Generating consensus sequence from bam file
fasta consensus bam
updated 6 months ago by 40k • written 4.6 years ago by 16k
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 6 months ago by 40k • written 4.3 years ago by ★ 15k
4
votes
2
replies
2.2k
views
Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 6 months ago by 40k • written 4.3 years ago by ★ 9.3k
50
votes
14
replies
75k
views
10 follow
Tutorial: Using R in Conda
R
updated 6 months ago by 40k • written 3.2 years ago by ▴ 750
33
votes
9
replies
30k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 6 months ago by 40k • written 3.1 years ago by ▴ 160
99
votes
16
replies
32k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 6 months ago by 40k • written 7.2 years ago by 26k
31
votes
6
replies
11k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 6 months ago by 40k • written 3.4 years ago by 86k
84
votes
47
replies
30k
views
28 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 2 days ago by 40k • written 10.0 years ago by ★ 7.7k
238
votes
176
replies
88k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 4 months ago by 40k • written 8.2 years ago by ★ 4.7k
8
votes
1
reply
1.2k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 6 months ago by 40k • written 2.5 years ago by 86k
21
votes
10
replies
6.0k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 6 months ago by 40k • written 3.1 years ago by 12k
12
votes
2
replies
1.2k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 6 months ago by 40k • written 2.5 years ago by 12k
149
votes
35
replies
60k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 7 months ago by 40k • written 10.8 years ago by ★ 1.6k
15
votes
2
replies
3.4k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 6 months ago by 40k • written 3.0 years ago by 3.0k
16
votes
7
replies
14k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 6 months ago by 40k • written 4.3 years ago by ▴ 310
288
votes
33
replies
99k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 7 months ago by 40k • written 9.9 years ago by 20k
5
votes
0
replies
4.1k
views
Tutorial: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates without alignment), mutate (create mutant genomes) and other miscellaneou…
bbmap
updated 6 months ago by 40k • written 2.7 years ago by 134k
11
votes
0
replies
5.8k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 6 months ago by 40k • written 2.7 years ago by 134k
10
votes
0
replies
3.8k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 6 months ago by 40k • written 2.7 years ago by 134k
11
votes
1
reply
2.5k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 6 months ago by 40k • written 2.7 years ago by ★ 25k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 6 months ago by 40k • written 9.5 years ago by ★ 1.9k
0
votes
1
reply
2.7k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 6 months ago by 40k • written 5.1 years ago by ▴ 310
6
votes
10
replies
4.8k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 6 months ago by 40k • written 5.6 years ago by ▴ 370
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 7 months ago by 40k • written 9.7 years ago by 6.0k
5
votes
3
replies
5.0k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 6 months ago by • 0 • written 5.9 years ago by ▴ 130
16
votes
11
replies
7.7k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
6 months ago by Ram 40k
48
votes
28
replies
8.6k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
4 months ago by Ram 40k
104
votes
6
replies
24k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 6 months ago by 40k • written 5.1 years ago by 16k
18
votes
40
replies
17k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 6 months ago by 40k • written 7.3 years ago by ▴ 170
24
votes
4
replies
6.9k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 6 months ago by 40k • written 4.1 years ago by 77k
15
votes
4
replies
4.3k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 6 months ago by 40k • written 3.2 years ago by ▴ 330
323 results • Page 2 of 7
Recent Votes
A: running RAxML and MrBayes over concatinated multiple sequence alignments
Comment: Weirdness in annotation (missing allele frequencies)
Comment: Weirdness in annotation (missing allele frequencies)
Comment: ncbi error report log for validate fastq issue
Comment: ncbi error report log for validate fastq issue
A: Bowtie2 MAPQ difference using local vs end-to-end alignment
C: Bowtie2 MAPQ difference using local vs end-to-end alignment
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Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Yes, I was confused as well. I think the same. Maybe Annovar uses some other resources besides gnomad, but it does not make sense. Also, I …
Comment: Weirdness in annotation (missing allele frequencies) by Can Abdullah • 0
Thank you so much, I decided to move forward as you suggested. Initially, I thought using the most up-to-date databases and positions would…
Comment: Getting the overlap between two GTF files by GenoMax 134k
Something in `AGAT` should work: https://agat.readthedocs.io/en/latest/?badge=latest
Answer: Automate the Splitting of a VCF File by Sample (bcftools) by Pierre Lindenbaum 157k
> My problem has been with trying to loop the process. ok here is a **nextflow** based solution,(NOT tested) workflow { …
Comment: Assessing Rockhopper's output by langziv ▴ 50
I see. I tried using the GUI Rockhopper for RNA-seq analysis of a K. pneumoniae strain, but the program didn't find the strain's assembly…
Answer: Getting the overlap between two GTF files by Pierre Lindenbaum 157k
bedtools intersect \ -a <(awk '/^[^#]/ {printf("%s\t%d\t%s\t%s\n",$1,int($4)-1,$5,$0);}' file1.gtf | sort -t $'\t' -k1,1 -k2…
Comment: Assessing Rockhopper's output by shelkmike ▴ 980
I used Rockhopper only for bacterial genomes assembled into circular contigs or circular scaffolds.
Comment: Unable to install HorvathMammalMethylChip40manifest packages by ATpoint 77k
There is no package of that name in CRAN or Bioconductor. Where do you have it from, so which tutorial you follow?
Comment: Subclustering of intergated cells from scRNA-seq data by fifty_fifty ▴ 60
thank you. This is exactly what I was looking for
Answer: Search RCSB with a list of protein names? by Mensur Dlakic ★ 25k
This is not the most elegant solution, but it should work with previous suggestions. In this remote directory: http://ftp.wwpdb.org/p…
Answer: Automate the Splitting of a VCF File by Sample (bcftools) by Ram 40k
The manual says you can split samples out at once using the `+split` plugin. So, `bcftools +split -Oz -o <PATH> file.vcf.gz` should do the …
Comment: differences between trajectories in conditions with Monocle3 or other tools by Amitm ★ 2.2k
Phate (or Monocle) doesn't do UMAP. If you have done UMAP already (using seurat) then you could use the cell barcode to UMAP cluster label …
Comment: Error: cannot open file 2 for reading From Cufflinks Version 2.2.1 When Attempti by Y • 0
I figured out how to make it work. The bams have to be comma separated not just by space: cd "${input_directory_with_associated_bam_fi…
Comment: Search RCSB with a list of protein names? by Joseph • 0
Hey, this is so close to what I'm looking for - I clarified in my edit. This is a great way to batch download lots of PDBs in RCSB by their…
Comment: Search RCSB with a list of protein names? by Joseph • 0
This is a really neat package, but I don't think it does exactly what I want, so I've clarified my question. This seems like it grabs a PD…
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