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323 results • Page 2 of 7
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4
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2
replies
2.1k
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Tutorial: Apply beagle5.0 to make imputation and phasing under CentOS and PBS
beagle5.0 beagle
updated 11 weeks ago by 39k • written 4.0 years ago by ★ 9.3k
45
votes
14
replies
65k
views
10 follow
Tutorial: Using R in Conda
R
updated 11 weeks ago by 39k • written 2.9 years ago by ▴ 690
31
votes
9
replies
26k
views
11 follow
Tutorial: installing samtools with conda - overcoming two common errors
samtools conda
updated 11 weeks ago by 39k • written 2.8 years ago by ▴ 140
99
votes
16
replies
30k
views
18 follow
Tutorial: Heatmaps in R
heatmap R
updated 11 weeks ago by 39k • written 6.8 years ago by 26k
21
votes
2
replies
4.1k
views
Tutorial: Extracting genomic feature sequences from GTF/GFF files with AGAT
extract GTF GFF sequence
updated 8 months ago by ▴ 40 • written 2.1 years ago by 7.9k
31
votes
6
replies
9.4k
views
Tutorial: A simple tutorial for a complex ComplexHeatmap
clustering pam arthritis ComplexHeatmap
updated 11 weeks ago by 39k • written 3.0 years ago by 85k
78
votes
42
replies
29k
views
25 follow
Tutorial: Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm rna-seq bioconductor
updated 24 days ago by 39k • written 9.6 years ago by ★ 7.7k
238
votes
176
replies
85k
views
73 follow
Tutorial: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq Survival TCGA
updated 8 days ago by 39k • written 7.8 years ago by ★ 4.6k
8
votes
1
reply
1.1k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 11 weeks ago by 39k • written 2.2 years ago by 85k
21
votes
10
replies
5.2k
views
Tutorial: Finding the significance of the overlap between 2 or more gene sets using simulation in R.
tidyverse gene R
updated 11 weeks ago by 39k • written 2.7 years ago by 12k
12
votes
2
replies
1.1k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 11 weeks ago by 39k • written 2.2 years ago by 12k
148
votes
35
replies
59k
views
33 follow
Tutorial: Tools For Metagenomic Data Analysis
metagenomics next-gen
updated 3 months ago by 39k • written 10.5 years ago by ★ 1.6k
14
votes
2
replies
3.0k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 11 weeks ago by 39k • written 2.7 years ago by 2.9k
4
votes
0
replies
1.9k
views
Tutorial: Building mosdepth on macOS
nim mosdepth
updated 11 weeks ago by 39k • written 3.1 years ago by 72k
16
votes
7
replies
13k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 11 weeks ago by 39k • written 4.0 years ago by ▴ 310
277
votes
33
replies
94k
views
25 follow
Tutorial: Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 3 months ago by 39k • written 9.6 years ago by 20k
5
votes
0
replies
3.7k
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 11 weeks ago by 39k • written 2.4 years ago by 129k
10
votes
0
replies
4.9k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 11 weeks ago by 39k • written 2.4 years ago by 129k
10
votes
0
replies
3.1k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 11 weeks ago by 39k • written 2.4 years ago by 129k
11
votes
1
reply
2.3k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 11 weeks ago by 39k • written 2.4 years ago by ★ 23k
40
votes
9
replies
11k
views
10 follow
Tutorial: Resources for flow cytometry bioinformatics
single-cell flow-cytometry
updated 12 weeks ago by 39k • written 9.1 years ago by ★ 1.9k
0
votes
1
reply
2.5k
views
Tutorial: Getting the lineage of an organism from NCBI taxonomy data
biosql python taxonomy
updated 11 weeks ago by 39k • written 4.8 years ago by ▴ 310
6
votes
10
replies
4.4k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 11 weeks ago by 39k • written 5.3 years ago by ▴ 360
43
votes
6
replies
11k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 3 months ago by 39k • written 9.3 years ago by 5.9k
5
votes
3
replies
4.7k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 11 weeks ago by • 0 • written 5.6 years ago by ▴ 130
16
votes
11
replies
7.5k
views
Tutorial: How to Use Biostars, Part II: Post types, Deleting, (Un)Subscribing, Linking and Bookmarking
meta how-to documentation
11 weeks ago by Ram 39k
45
votes
28
replies
7.3k
views
9 follow
Tutorial: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
documentation meta how-to
14 days ago by Ram 39k
101
votes
6
replies
23k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 11 weeks ago by 39k • written 4.7 years ago by 16k
18
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 11 weeks ago by 39k • written 6.9 years ago by ▴ 170
23
votes
4
replies
6.4k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 11 weeks ago by 39k • written 3.8 years ago by 72k
15
votes
4
replies
4.2k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 11 weeks ago by 39k • written 2.8 years ago by ▴ 310
26
votes
0
replies
2.1k
views
Tutorial: Resources / databases for clinical interpretation of cancer variants
interpretation cancer annotation variant
updated 11 weeks ago by 39k • written 3.6 years ago by 19k
10
votes
1
reply
2.1k
views
Tutorial: introduce a tool for fast identification of SARS-CoV-2 and other microbes from sequencing data
SARS-CoV-2 fastv COVID-19
updated 11 weeks ago by 39k • written 3.2 years ago by ★ 2.4k
60
votes
52
replies
40k
views
23 follow
Tutorial: Creating Interactive Volcano Plots with R and Plot.ly
plotly R volcano-plot
updated 11 weeks ago by 39k • written 6.7 years ago by ★ 3.3k
12
votes
7
replies
4.8k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 11 weeks ago by 39k • written 2.7 years ago by 85k
18
votes
22
replies
7.4k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 11 weeks ago by 39k • written 3.5 years ago by 7.9k
0
votes
0
replies
894
views
Tutorial: BrainArray CDF, annotation, etc
db brainarray cdf
updated 11 weeks ago by 39k • written 2.7 years ago by 85k
12
votes
0
replies
2.2k
views
Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 11 weeks ago by 39k • written 2.8 years ago by 12k
76
votes
70
replies
16k
views
18 follow
Tutorial: Clustering of DAVID gene enrichment results from gene expression studies
enrichment david
updated 11 weeks ago by 39k • written 5.3 years ago by 85k
1
vote
1
reply
1.1k
views
Tutorial: Downloading GnuWin and using to convert txt to bed file for windows users
bed bed2txt sequencing txt
updated 11 weeks ago by 39k • written 2.8 years ago by • 0
4
votes
3
replies
4.0k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 11 weeks ago by 39k • written 5.1 years ago by ★ 3.9k
4
votes
1
reply
1.1k
views
Tutorial: Real World BEDtools. Practical Examples for Variant Filtering and Gene Annotations
BED BEDtools
updated 11 weeks ago by 39k • written 2.8 years ago by ▴ 40
3
votes
0
replies
3.0k
views
Tutorial: Sorting GFF/GTF files
gtf gff
updated 12 weeks ago by 39k • written 2.9 years ago by 7.9k
20
votes
6
replies
5.0k
views
Tutorial: Open Targets and programmatic access
open-targets disease API drug
updated 11 weeks ago by 39k • written 6.7 years ago by ★ 5.2k
2
votes
2
replies
1.6k
views
Tutorial: Human mitochondrial DNA annotation in SnpEff
chrMT SNP snpEff
updated 11 weeks ago by 39k • written 2.9 years ago by 3.2k
12
votes
5
replies
1.9k
views
Tutorial: FASTA file split
fasta
updated 11 weeks ago by 39k • written 3.0 years ago by 7.9k
0
votes
0
replies
1.3k
views
Tutorial: VIDEO: Installing BLAST Databases on Your Own Computer
BLAST-databases Linux sequence MacOSX
updated 11 weeks ago by 39k • written 3.0 years ago by ▴ 450
0
votes
0
replies
829
views
Tutorial: VIDEO: BLAST Searches Through a Data Science Lens
Covid19 Data-Science sequence BLAST
updated 11 weeks ago by 39k • written 3.0 years ago by ▴ 450
2
votes
1
reply
1.3k
views
Tutorial: A very simple way to detect viruses and microorganisms from mNGS FASTQ data using fastv
SARS-CoV-2 fastv COVID-19 viruses
updated 11 weeks ago by 39k • written 3.0 years ago by ★ 2.4k
70
votes
26
replies
25k
views
15 follow
Tutorial: How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 3 months ago by 39k • written 9.3 years ago by 98k
323 results • Page 2 of 7
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Comment: RNASeq gene labeling and mRNA filter from bulkRNA data. by ATpoint 72k
This information is annotated in GTF files. You can get them for almost every annotated species from Ensembl. There is a column `gene_bioty…
Answer: DE genes across multiple scRNAseq clusters-are they significantly enriched? by ATpoint 72k
First of all, with thousands of DEGs you might want to choose a DE framework that allows testing against a fold change threshold, such as `…
Comment: PacBio Pipeline and Tools for Variant Call by Kiran ▴ 80
Thanks a lot William, I am Clear now
Comment: The famous WGS dataset, Ashkenazi Trio? by cmdcolin ★ 3.0k
what is valuable information to you
Answer: Why weblogo of biopython doesn't work? by minakshiboruahassam • 0
The weblogo3 application is giving same file even if u run the scripts separately on python standalone or whatever. The weblogo command is …
Answer: Make a BedGraph file by rfran010 ▴ 80
I would suggest bedtools makewindows to generate your 3,000bp bins then bedtools coverage to generate fraction of repeats over your windows…
Answer: What is the best way to clean bulk RNA-seq data? by rfran010 ▴ 80
Honestly, I am a fan of visualizing to select a threshold since these can depend on the specific experiment. I would even just run standard…
Answer: Help with running ATAC using Encode pipeline by rfran010 ▴ 80
Read all instructions carefully Specifically, this info is under the "Input JSON file specification" section with details in the followin…
Answer: BioInformatics, Software by rfran010 ▴ 80
There have been some good suggestions, but it seems like you may be asking one of two questions, either (1) how to do bioinformatics? or (2…
Answer: Genome assembly statistical tools by Bryan • 0
I'll follow up what a few others have mentioned, but I like stats.sh within the BBTools package for raw assembly stats. I'll then polish my…
Comment: how to design a guide RNA by rfran010 ▴ 80
I agree this is very basic CRISPR mechanism and you'd be better off reading sites that could explain better than me. However, there is a lo…
Comment: ATAC peak-calling: same peak ID across multiple experimental conditions? by rfran010 ▴ 80
You want to use the MACS2 score columns? You can retain these with bedtools option `-c` . This will retain the score columns from any merge…
Comment: best annotation approach for peaks by rfran010 ▴ 80
The number of regions annotated as "Promoters" is the same regardless of TSS length? You can add this argument to annotatePeak (for mouse M…
Answer: Optimum setting for local blastp for ~10K sequences by GenoMax 129k
It is possible that NCBI keeps the entire `nr` indexes in memory and searches against that so there is no I/O involved. NCBI now also uses …
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10x does give you a big flashing warning telling you what the new default is, and tells you how to redo it without that if it's not what yo…
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