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131 results • Page 2 of 3
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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 10 days ago by 38k • written 4.4 years ago by ▴ 740
20
votes
4
replies
2.2k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 10 days ago by 38k • written 3.9 years ago by ▴ 180
19
votes
9
replies
6.0k
views
8 follow
Tutorial: Interactive Perl Learning
perl
updated 25 days ago by 38k • written 9.8 years ago by 9.5k
19
votes
4
replies
8.4k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 29 days ago by 38k • written 10.1 years ago by 97k
18
votes
22
replies
7.1k
views
10 follow
Tutorial: Create de novo repeat library
de-novo repeat annotation
updated 10 days ago by 38k • written 3.3 years ago by 7.7k
17
votes
40
replies
16k
views
16 follow
Tutorial: Easy way to run easily orthoMCL (Copy & paste)
all-v-all orthomcl
updated 10 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
10 days ago by Ram 38k
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 10 days ago by 38k • written 6.4 years ago by ★ 4.6k
16
votes
7
replies
12k
views
Tutorial: Integrating VDJ sequencing data with Seurat
VDJ Seurat sc-RNAseq clonotyping
updated 10 days ago by 38k • written 3.8 years ago by ▴ 310
15
votes
5
replies
11k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 15 days ago by 38k • written 5.3 years ago by ▴ 740
15
votes
2
replies
2.7k
views
Tutorial: Introduction to bedtools.
bedtools
updated 15 days ago by 38k • written 8.3 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 10 days ago by 38k • written 2.7 years ago by ▴ 300
14
votes
7
replies
5.4k
views
Tutorial: Visualization of ChIP-Seq peak overlaps using HOMER mergePeaks and UpSetR
ChIP-Seq peaks R HOMER
updated 10 days ago by 38k • written 6.9 years ago by ★ 3.3k
14
votes
2
replies
2.8k
views
Tutorial: Methylation Analysis Tutorial in R_part2
cancer methylation RNA-Seq R
updated 10 days ago by 38k • written 2.5 years ago by 2.9k
12
votes
2
replies
1.0k
views
Tutorial: Factors in R - How do they work, and how did I break my data?
R
updated 10 days ago by 38k • written 2.0 years ago by 11k
12
votes
1
reply
4.8k
views
Tutorial: scRNA-seq CITE-seq-count bioinformatics
CITE-seq-count scRNA-seq RNA-Seq
updated 10 days ago by 38k • written 3.0 years ago by 4.6k
12
votes
31
replies
4.7k
views
6 follow
Tutorial: gene set filter/selection for training ab initio annotation tools
geneset genome gene abinitio
updated 15 days ago by 38k • written 3.6 years ago by 7.7k
12
votes
5
replies
1.8k
views
Tutorial: FASTA file split
fasta
updated 10 days ago by 38k • written 2.8 years ago by 7.7k
12
votes
4
replies
1.8k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 1 day ago by 38k • written 5.5 years ago by ▴ 570
12
votes
20
replies
11k
views
10 follow
Tutorial: Associating VDJ clonotyping data with scRNA-seq in Seurat
single-cell RNA-Seq seurat TCR
updated 10 days ago by 38k • written 3.8 years ago by ★ 14k
12
votes
0
replies
2.0k
views
Tutorial: Long versus wide data for plotting genomics data in R.
ggplot2 tidyverse data.table R
updated 10 days ago by 38k • written 2.6 years ago by 11k
11
votes
1
reply
2.2k
views
Tutorial: Guidelines for the computational analysis of single-cell RNA sequencing data
scRNA-seq
updated 10 days ago by 38k • written 2.2 years ago by ★ 23k
10
votes
5
replies
18k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 10 days ago by 38k • written 4.7 years ago by ★ 9.3k
10
votes
7
replies
4.4k
views
Tutorial: STARsolo config for 10x Chromium v1, v2, v3
Chromium 10x STARsolo STAR
updated 10 days ago by 38k • written 2.5 years ago by 84k
10
votes
0
replies
2.7k
views
Tutorial: Yes .. BBMap can do that! - Part I : bbmap (aligner), bbduk (scan/trim), repair (fix PE reads) and reformat (format conversions)
bbmap
updated 10 days ago by 38k • written 2.2 years ago by 127k
10
votes
1
reply
2.0k
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 10 days ago by 38k • written 3.0 years ago by ★ 2.4k
10
votes
0
replies
4.4k
views
Tutorial: Yes .. BBMap can do that! - Part II randomreads (read simulation), demuxbyname/filterbyname, bbsplit (read binning/decontamination) and pileup (cover…
bbmap
updated 10 days ago by 38k • written 2.2 years ago by 127k
9
votes
4
replies
9.0k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 10 days ago by 38k • written 3.7 years ago by 4.6k
8
votes
9
replies
10k
views
Tutorial: Extracting subset of records from FASTA/FASTQ files based on exact/pattern matches of IDs (ONE-LINERS)
fastq fasta
updated 18 days ago by 38k • written 8.9 years ago by ★ 1.8k
8
votes
1
reply
1.0k
views
Tutorial: Split a 'linearised' (flattened) FASTA sequence into multi-line using AWK
fasta awk
updated 10 days ago by 38k • written 2.0 years ago by 84k
8
votes
19
replies
12k
views
9 follow
Tutorial: A:orthomcl with local mysql server on linux server, complete install
mysql orthomcl
updated 15 days ago by 38k • written 8.3 years ago by ▴ 580
7
votes
2
replies
3.3k
views
Tutorial: List Of Tools For Mapping High-Throughput Sequencing Data (2012)
next-gen mapping
updated 29 days ago by 38k • written 10.5 years ago by 11k
7
votes
0
replies
4.5k
views
Tutorial: How To Perform A Hierarchical Clustering Using Interactive Heatmaps From Gitools?
clustering
updated 21 days ago by 38k • written 9.0 years ago by ▴ 990
6
votes
0
replies
1.3k
views
Tutorial: NCBI dbVar releases updated human reference structural variation (SV) data files and tutorials
dbvar structural-variation
updated 7 days ago by 38k • written 4.4 years ago by ▴ 70
6
votes
1
reply
2.8k
views
Tutorial: Practical Guidelines for the Comprehensive Analysis of ChIP-seq Data
ChIP-Seq peak-calling sequencing
updated 18 days ago by 38k • written 8.9 years ago by ▴ 220
6
votes
4
replies
6.9k
views
Tutorial: Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization ChIP-seq RNA-seq ucsc-genome-browser bigwig
updated 29 days ago by 38k • written 10.0 years ago by 11k
6
votes
0
replies
3.4k
views
Tutorial: How to predict genes using a two-pass (iterative) MAKER2 workflow
Assembly
updated 18 days ago by 38k • written 8.8 years ago by 7.7k
6
votes
2
replies
2.4k
views
Tutorial: Tutorial Bioinformatics Static Website
website
updated 22 days ago by 38k • written 9.1 years ago by ▴ 610
6
votes
3
replies
4.1k
views
Tutorial: Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment sequencing RNA-seq gene
updated 9 days ago by 38k • written 4.4 years ago by ▴ 40
6
votes
10
replies
4.3k
views
Tutorial: Differentially methylated regions: Easy & Fast Identification and ANnoTation
DMR dna-methylation
updated 10 days ago by 38k • written 5.1 years ago by ▴ 340
5
votes
1
reply
1.7k
views
Tutorial: A Guide to DNA Sequencing Techniques Part 1
dna sanger sequencing pyrosequencing
updated 14 hours ago by 38k • written 7.7 years ago by ▴ 370
5
votes
3
replies
3.9k
views
Tutorial: Chip Seq Review Papers
chip-seq
updated 29 days ago by 38k • written 10.3 years ago by ▴ 80
5
votes
0
replies
3.5k
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 10 days ago by 38k • written 2.2 years ago by 127k
5
votes
0
replies
2.6k
views
Tutorial: How to run CWL with Nextflow
cwl nextflow
updated 10 days ago by 38k • written 3.1 years ago by ★ 3.3k
5
votes
1
reply
2.3k
views
Tutorial: Nice simple interactive Vim tutorial
vim linux
updated 15 days ago by 38k • written 8.4 years ago by 9.5k
5
votes
2
replies
2.0k
views
Tutorial: Using Bedtools Closest (closestBed) to make distance histograms of protein binding frequency near all types of pre-RNA junctions (e.g. exon-intron an…
preRNA closestBed bedtools-closest bedtools
updated 10 days ago by 38k • written 4.2 years ago by ▴ 10
5
votes
3
replies
4.5k
views
Tutorial: bam2rpkm by bedtools
bam RNA-Seq bedtools rpkm
updated 8 days ago by • 0 • written 5.4 years ago by ▴ 130
5
votes
2
replies
2.0k
views
Tutorial: NCBI submissions: SRA and TSA
NCBI TSA SRA RNA-Seq
updated 7 days ago by 38k • written 4.3 years ago by ▴ 50
5
votes
0
replies
1.8k
views
Tutorial: Gatk December Workshop Presentations
gatk
updated 29 days ago by 38k • written 10.2 years ago by ★ 5.2k
4
votes
2
replies
3.3k
views
Tutorial: Introduce OpenGene: an open source library for processing NGS data
NGS sequencing Julia OpenGene
updated 9 days ago by 38k • written 7.1 years ago by ★ 2.4k
131 results • Page 2 of 3
Recent Votes
Difference between RNA-sq and Transcriptome
Rat lung transcriptome
A: microarray, RNAseq, CEL, edgeR, etc. for DGE analysis
Converting SNP from chr:pos to rs number using PLINK?
How do I explain the difference between edgeR, LIMMA, DESeq etc. to experimental Biologist/non-bioinformatician
Answer: Cellranger sequencing
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ?
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Popular Question to bitpir ▴ 210
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Recent Replies
Comment: Remove part of headers in FASTA file by Pierre Lindenbaum 153k
Use `cut -d ' '`
Answer: Problem running interproscan-5.15-54.0 for protein sequences by Pratyay • 0
Hi, can you guide me how to compile the src folder? Many thanks!
Comment: Matching gene-expression data with clinical data: best practices. by krushnach80 ★ 1.1k
You can check [this][1] [1]: https://www.linkedomics.org/
Answer: Matching gene-expression data with clinical data: best practices. by jose.sgomez94 • 0
Figured out one can use the TCGAutils package in R and UUIDtobarcode() function. Still, suggestions of best practices would be awesome!
Answer: Understanding multifactor designs and control variables in DESeq2 by FrankStarling ▴ 50
https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2021/RNAseq/Markdowns/10_DE_analysis_with_DESeq2.Solutions.html …
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? by Adaline.D • 0
I appreciate your help, LChart! I will use raw data in case of a substantial loss of power. (1) The publication did a PCA and then analy…
Answer: Is it possible to do DGE analysis using log 2 normalized data with EdgeR ? by LChart 2.2k
Short answer: use LIMMA Long answer: edgeR uses a negative binomial model, and expects *counts* and not *values*. Please read section 2.8.…
Comment: Python formatting when visualizing Primer3-py dimers by bhumm ▴ 30
Wayne, both of these methods work beautifully. I really appreciate the detail you provided, thank you so much for your help!
Comment: Ortholog assembly and extraction by dthorbur ▴ 420
I really like `orthofinder` and use it frequently, but there are also plenty of other tools out there. [Here](https://academic.oup.com/mbe/…
Comment: chloroplast genome gaps by ugur • 0
after alignment, it occurs in different sizes of gaps
Answer: Cellranger sequencing by ATpoint 70k
Not that I am aware of. Unlike methods such as salmon it does genome alignment and does not resolve the exact transcript expression composi…
Answer: Assembly at lineage level from shotgun data ? by Mensur Dlakic ★ 23k
The paper I list below is meant for improving the existing MAG assemblies. Yet the program will do what you want: if you give it a referenc…
Comment: Ortholog assembly and extraction by GenoMax 127k
Many seem to use `orthofinder` for this purpose. See if it is useful: https://github.com/davidemms/OrthoFinder
Answer: Python formatting when visualizing Primer3-py dimers by Wayne ★ 1.7k
Try this so you'll see that using [tabulate](https://github.com/astanin/python-tabulate) to print the dataframe causes it to respect the li…
Comment: Python formatting when visualizing Primer3-py dimers by bhumm ▴ 30
Glad I am making this more clear. The 'test1' in practice will be the 'primer name' to allow for tracking of other metrics (Tm, hairpin str…
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