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329 results • Page 1 of 7
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10
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5
replies
411
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Tutorial: Installing an updated R version (>=4.0) using conda
R software error Tutorial
updated 2 days ago by 49k • written 8 weeks ago by ▴ 530
22
votes
11
replies
4.7k
views
7 follow
Tutorial: Using R in Conda
R Tutorial
updated 9 days ago by ★ 2.9k • written 9 months ago by ▴ 330
13
votes
4
replies
4.3k
views
6 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda Tutorial
updated 10 days ago by 49k • written 9 months ago by ▴ 70
85
votes
16
replies
22k
views
18 follow
Tutorial: Heatmaps in R
heatmap R Tutorial
updated 12 days ago by • 0 • written 4.8 years ago by 24k
68
votes
63
replies
16k
views
17 follow
Tutorial: Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
PLINK 1000 PCA genomes Tutorial
22 hours ago by Kevin Blighe 73k
5
votes
1
reply
176
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 25 days ago by 48k • written 25 days ago by ★ 5.7k
22
votes
4
replies
2.6k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
complexheatmap clustering arthritis pam Tutorial
updated 29 days ago by ▴ 40 • written 11 months ago by 73k
67
votes
38
replies
21k
views
22 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
rna-seq bioconductor fpkm Forum Tutorial
updated 4 weeks ago by • 0 • written 7.6 years ago by ★ 7.3k
69
votes
1
reply
45k
views
Tutorial: How To Ask Good Questions On Technical And Scientific Forums
tutorial Tutorial
written 7.9 years ago by 11k
6
votes
0
replies
273
views
Tutorial: Pipes in R: An introduction and some advanced tips and tricks.
R
6 weeks ago by rpolicastro 5.2k
225
votes
175
replies
68k
views
72 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq TCGA Survival Tutorial
updated 7 weeks ago by 33k • written 5.8 years ago by ★ 4.3k
10
votes
0
replies
564
views
Tutorial: Greatly speed up conda by using mamba
software
7 weeks ago by rpolicastro 5.2k
6
votes
0
replies
198
views
Tutorial: data.frames in R: How vectorization can save you time and heartache
R
6 weeks ago by rpolicastro 5.2k
7
votes
1
reply
191
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
awk fasta Tutorial
8 weeks ago by Kevin Blighe 73k
10
votes
6
replies
946
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
R tidyverse gene Tutorial
updated 8 weeks ago by ▴ 730 • written 8 months ago by 5.2k
12
votes
2
replies
273
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R Tutorial
6 weeks ago by rpolicastro 5.2k
144
votes
34
replies
50k
views
31 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen tutorial Tutorial
updated 8 weeks ago by ▴ 120 • written 8.5 years ago by ★ 1.6k
4
votes
2
replies
1.1k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
R linux bioinformatics Tutorial
updated 8 weeks ago by • 0 • written 3 months ago by ▴ 40
10
votes
2
replies
864
views
Tutorial: Methylation Analysis Tutorial in R_part2
methylation RNA-Seq R cancer Tutorial
9 weeks ago by Hamid Ghaedi ★ 1.3k
4
votes
0
replies
598
views
Tutorial: Building mosdepth on macOS
mosdepth nim Tutorial
5 weeks ago by ATpoint 49k
13
votes
0
replies
3.0k
views
Tutorial: Methylation Analysis Tutorial in R_part1
methylation cancer R Tutorial
10 weeks ago by Hamid Ghaedi ★ 1.3k
69
votes
32
replies
9.9k
views
17 follow
Tutorial: Enrichment Analysis, Clustering and Scoring with pathfindR
R pathway enrichment active subnetwork Tutorial
updated 11 weeks ago by • 0 • written 2.9 years ago by ★ 1.1k
42
votes
16
replies
4.2k
views
9 follow
Tutorial: Generating consensus sequence from bam file
bam consensus fasta Tutorial
updated 4 days ago by ▴ 760 • written 2.2 years ago by 14k
11
votes
7
replies
5.7k
views
Tutorial: Integrating VDJ sequencing data with Seurat
Seurat clonotyping VDJ sc-RNAseq Tutorial
updated 12 weeks ago by 7.0k • written 23 months ago by ▴ 260
231
votes
32
replies
68k
views
22 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates tutorial Tutorial
updated 12 weeks ago by ▴ 10 • written 7.6 years ago by 19k
40
votes
8
replies
2.7k
views
9 follow
Tutorial: Gene Set Enrichment Analysis
microarray RNA-Seq Tutorial enrichment GSEA
5 weeks ago by Hamid Ghaedi ★ 1.3k
3
votes
0
replies
521
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
3 months ago by GenoMax 101k
6
votes
0
replies
1.2k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap Tutorial
3 months ago by GenoMax 101k
7
votes
0
replies
755
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap Tutorial
3 months ago by GenoMax 101k
8
votes
1
reply
527
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq Tutorial
updated 4 months ago by 49k • written 4 months ago by ★ 11k
34
votes
9
replies
8.9k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
tutorial flow cytometry Tutorial single cell
written 7.1 years ago by ★ 1.9k
2
votes
0
replies
700
views
Tutorial: Best Python Course
python Tutorial ad
updated 4 months ago by 15k • written 4 months ago by ▴ 20
0
votes
1
reply
1.6k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
taxonomy python biosql Tutorial
updated 5 months ago by • 0 • written 2.8 years ago by ▴ 220
70
votes
13
replies
12k
views
12 follow
Tutorial: Exploring cancer mutation data portals
Cancer Data Portal Mutation TCGA ICGC Tutorial
5 months ago by Malachi Griffith 18k
4
votes
10
replies
2.9k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
dna methylation Tutorial DMR
5 months ago by dec986 ▴ 270
41
votes
6
replies
9.6k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
maf vcf ensembl tcga somatic Tutorial
5 months ago by Cyriac Kandoth 5.5k
5
votes
2
replies
2.8k
views
Tutorial: bam2rpkm by bedtools
RNA-Seq bam rpkm bedtools Tutorial
updated 5 months ago by 49k • written 3.6 years ago by ▴ 110
16
votes
11
replies
4.8k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation Tutorial
5 months ago by Ram 33k
40
votes
33
replies
5.0k
views
8 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
meta how-to documentation Tutorial
5 months ago by Ram 33k
83
votes
6
replies
14k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
snakemake conda workflow Tutorial
updated 6 months ago by ▴ 30 • written 2.7 years ago by 14k
15
votes
40
replies
12k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
run easy orthomcl all-v-all mcl Tutorial
updated 6 months ago by ★ 1.8k • written 4.9 years ago by ▴ 140
19
votes
5
replies
3.5k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
enrichedheatmap chip-seq atac-seq heatmap Tutorial
27 days ago by ATpoint 49k
9
votes
4
replies
2.3k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
RNA-Seq Transcriptomics Tutorial R bioconductor
7 months ago by Thind amarinder ▴ 170
24
votes
0
replies
1.4k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
variant interpretation annotation clinical cancer Tutorial
7 months ago by Malachi Griffith 18k
10
votes
1
reply
1.3k
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
7 months ago by chen ★ 2.1k
54
votes
49
replies
32k
views
22 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
R plotly volcano plot Tutorial
updated 3 days ago by 33k • written 4.6 years ago by ★ 2.9k
9
votes
5
replies
1.1k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
STAR STARsolo 10x Chromium Tutorial
7 months ago by Kevin Blighe 73k
13
votes
16
replies
2.8k
views
7 follow
Tutorial: Create de novo repeat library
annotation repeat de-novo Tutorial
7 months ago by Juke34 ★ 5.7k
0
votes
0
replies
306
views
Tutorial: BrainArray CDF, annotation, etc
brainarray cdf db Tutorial
8 months ago by Kevin Blighe 73k
32
votes
0
replies
2.6k
views
Tutorial: Basic normalization, batch correction and visualization of RNA-seq data
RNA-Seq batch correction edgeR ma-plot Tutorial
8 months ago by ATpoint 49k
329 results • Page 1 of 7
Recent Votes
Answer: Error in running miRDeep2
Comment: Snakemake and STARsolo
Comment: Snakemake and STARsolo
Answer: Bedtools intersect 0- and 1-based coordinate files
Answer: Bedtools intersect 0- and 1-based coordinate files
A: Gene Set Analysis Software That Takes A Vcf As Input
C: deseq2 replicates error
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Recent Replies
Comment: How to extract translated sequence of a partcular gene by parsing GenBank file by cpad0112 15k
check if following code works out (be mindful of copying errors from web): import sys from Bio import SeqIO gbinput= sys.argv[…
Answer: collapsing coordinate information from a blast result by Mensur Dlakic ★ 11k
I think this program does almost exactly what you want. https://sourceforge.net/projects/weinberg-overcluster2/
Comment: Snakemake and STARsolo by Jeremy Leipzig 20k
i think `SAMPLES ,= glob_wildcards` is valid but i do prefer to know what I am trying to make rather than let a directory run the show http…
Comment: Snakemake and STARsolo by Ram 33k
Follow Jeremy's advice. Your Snakefile is badly formed and the line outside the rule breaks everything.
Comment: What is a difference between uniprot and 'nr. Non-redundant GenBank...'? by Dunois ▴ 780
I'd add to @genomax 's point that if you're going to run a search against `NR` on a local machine, it's probably unwise at this point to us…
Comment: Bedtools intersect 0- and 1-based coordinate files by maxrwjones898 ▴ 10
Ah wonderful, good to know! Brilliant answer and thanks for the code / outputs to back it up.
Comment: What is a difference between uniprot and 'nr. Non-redundant GenBank...'? by GenoMax 101k
> clients proprietary sequences which cannot by processed on public > website. No option but to download `nr` indexes and do the search lo…
Comment: What is a difference between uniprot and 'nr. Non-redundant GenBank...'? by matt ▴ 10
I would like to be able to do ‘blastp’ with clients proprietary sequences which cannot by processed on public website. Until now I did it …
Answer: Bedtools intersect 0- and 1-based coordinate files by ATpoint 49k
> Does bedtools intersect automatically take this difference into account? Yes, it is quite a smart one. Example (BED vs GTF, random file…
Comment: Issue on downloading fastPHASE in Mac by 4galaxy77 ▴ 510
Out of polite curiosity, what use to people have for fastPHASE in 2021? I believe it's still the most accurate method, but pretty slow. So …
Comment: Snakemake and STARsolo by Jeremy Leipzig 20k
one of them is `{sample}.Aligned.out.sam`. Start by creating a target variable that point to the sam files you want produced SAMPLES =…
Comment: T-test analysis for gene expression comparison by bioinformatics2020 ▴ 580
THIS! You need to go back and learn about what type of distribution is used for a t-test. Then start understanding the distributions that g…
Comment: Warning messages: In svgStyleAttributes(style, svgdev) : Removing non-S by xxxxxxxx ▴ 20
arrayQualityMetrics version- 3.47.0
Comment: Liftover vcf file from hs37d5 assembly to b37 assembly by Pierre Lindenbaum 135k
don't you just have to rename the chromosomes (if needed) and discard the chromosomes that are not present in the other reference ?
Answer: How to extract translated sequence of pol gene from a GenBank file by GenoMax 101k
This is a duplicate post of a question already asked here --> https://www.biostars.org/p/9470184 Please use the other post. This post will…
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