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411 results • Page
3 of 9
Sort: replies
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Views
Votes
Replies
13
votes
6
replies
6.0k
views
Tutorial:
Trim & align paired-end reads in a single pass
align
trim
fastq
pipe
paired-end
updated 12 months ago by
Ram
43k • written 7.9 years ago by
dariober
14k
32
votes
6
replies
12k
views
Tutorial:
A simple tutorial for a complex ComplexHeatmap
clustering
pam
arthritis
ComplexHeatmap
updated 13 months ago by
Ram
43k • written 3.9 years ago by
Kevin Blighe
87k
16
votes
6
replies
6.4k
views
Tutorial:
How to make your snakefiles self-documenting
snakemake
updated 12 months ago by
Ram
43k • written 7.5 years ago by
Botond Sipos
★ 1.7k
12
votes
6
replies
5.0k
views
Tutorial:
sharing some naive codes for microarray normalization in R with whom are too new in R alike me
R
updated 21 months ago by
Ram
43k • written 8.2 years ago by
zizigolu
★ 4.3k
2
votes
6
replies
3.2k
views
Tutorial:
Rembrandt Glioma Data Analysis (PART I) - Are Gender specific genes related to cancer ?
gene
R
Rembrandt
updated 12 months ago by
Ram
43k • written 7.8 years ago by
majuang66
▴ 140
106
votes
6
replies
26k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 13 months ago by
Ram
43k • written 5.6 years ago by
finswimmer
16k
30
votes
6
replies
22k
views
Tutorial:
Transforming And Manipulating Color Space Reads
conversion
solid
updated 19 months ago by
Ram
43k • written 12.0 years ago by
Istvan Albert
100k
61
votes
6
replies
9.5k
views
Tutorial:
Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 14 months ago by
Ram
43k • written 10.7 years ago by
Medhat
9.7k
2
votes
5
replies
2.2k
views
Tutorial:
Building OMA database on SGE
oma
updated 12 months ago by
Ram
43k • written 7.8 years ago by
javier.herrero
▴ 10
16
votes
5
replies
9.0k
views
Tutorial:
Using The Biomart Perl Api For Simple Queries
api
perl
biomart
updated 14 months ago by
Ram
43k • written 11.6 years ago by
Obi Griffith
20k
10
votes
5
replies
23k
views
Tutorial:
Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 13 months ago by
Ram
43k • written 5.8 years ago by
Shicheng Guo
★ 9.4k
29
votes
5
replies
6.4k
views
Tutorial:
Gnu Parallel Tutorial
parallel
gnu-parallel
updated 14 months ago by
Ram
43k • written 10.6 years ago by
ole.tange
★ 4.4k
15
votes
5
replies
15k
views
Tutorial:
How to create a mutation lolliplot with GenVisR
bioconductor
graphics
R
genvisr
updated 12 months ago by
Ram
43k • written 7.9 years ago by
Obi Griffith
20k
12
votes
5
replies
8.4k
views
Tutorial:
How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 12 months ago by
Ram
43k • written 7.9 years ago by
Shicheng Guo
★ 9.4k
21
votes
5
replies
6.8k
views
Tutorial:
Analysis of single-cell RNA-seq data
single-cell
RNA-Seq
updated 12 months ago by
Ram
43k • written 7.8 years ago by
Geparada
★ 1.5k
5
votes
5
replies
6.9k
views
Tutorial:
use firehose_get to download TCGA data
tcga
RNA-Seq
updated 11 months ago by
Ram
43k • written 6.5 years ago by
jmzeng1314
▴ 130
9
votes
5
replies
2.3k
views
Tutorial:
What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 11 months ago by
Ram
43k • written 6.8 years ago by
Istvan Albert
100k
54
votes
5
replies
15k
views
6 follow
Tutorial:
Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 19 months ago by
Ram
43k • written 10.4 years ago by
Nicholas Spies
★ 1.2k
12
votes
5
replies
2.4k
views
Tutorial:
FASTA file split
fasta
updated 13 months ago by
Ram
43k • written 3.9 years ago by
Juke34
8.5k
16
votes
5
replies
13k
views
6 follow
Tutorial:
Easy way to do GO enrichment in R
enrichr
RNA-Seq
gene
R
updated 13 months ago by
Ram
43k • written 6.4 years ago by
ahmad mousavi
▴ 800
70
votes
5
replies
11k
views
8 follow
Tutorial:
Bioinformatics For Metagenomic Analyses
QC
taxonomy
metagenomics
updated 2.1 years ago by
Ram
43k • written 10.1 years ago by
umer.zeeshan.ijaz
★ 1.8k
37
votes
5
replies
6.1k
views
Tutorial:
[Beginner] Introduction to bioinformatics file types
fastq
fasta
bed
SAM
updated 7 months ago by
gallardodiazmiriam
▴ 20 • written 8.8 years ago by
Luke Crichton
▴ 430
64
votes
5
replies
7.3k
views
10 follow
Tutorial:
Informatics of RNA-Seq.
next-gen
RNA-Seq
updated 18 months ago by
Ram
43k • written 8.7 years ago by
GouthamAtla
12k
1
vote
5
replies
611
views
Tutorial:
Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq
TOSICA
updated 3 months ago by
Ram
43k • written 3 months ago by
Julia Ma
▴ 120
12
votes
4
replies
5.4k
views
Tutorial:
*FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux
R
updated 14 months ago by
Ram
43k • written 3.2 years ago by
garden_giessen
▴ 130
3
votes
4
replies
4.5k
views
Tutorial:
gencore: a tool to reduce sequencing noises by generating consensus reads
consensus
OpenGene
sequencing-noise
updated 11 months ago by
Ram
43k • written 6.0 years ago by
chen
★ 2.5k
3
votes
4
replies
3.6k
views
Tutorial:
Gene Set Enrichment Analysis on T-BioInfo
gene
RNA-Seq
updated 11 months ago by
Ram
43k • written 5.5 years ago by
elia.brodsky
▴ 340
1
vote
4
replies
3.5k
views
Tutorial:
How to install C++ compilers/make from GNU for Gromacs?
Gromacs
Cpp-compilers
GNU
updated 12 months ago by
Ram
43k • written 7.9 years ago by
Hassan Rasouli
▴ 10
9
votes
4
replies
5.5k
views
Tutorial:
Unsupervised clustering on gene expression data
gene-expression
clustering
RNA-seq
8 months ago by
Hamid Ghaedi
3.2k
29
votes
4
replies
4.5k
views
Tutorial:
Modern Statistics for Modern Biology
statistics
updated 13 months ago by
Ram
43k • written 5.3 years ago by
Jean-Karim Heriche
27k
20
votes
4
replies
14k
views
Tutorial:
How To Install A Specific Cdf Package For Use In Bioconductor
bioconductor
affymetrix
updated 14 months ago by
Ram
43k • written 11.1 years ago by
Obi Griffith
20k
1
vote
4
replies
3.4k
views
Tutorial:
Applying machine learning to NGS transcriptomic data
next-gen
RNA-Seq
updated 11 months ago by
Ram
43k • written 6.0 years ago by
elia.brodsky
▴ 340
32
votes
4
replies
7.9k
views
Tutorial:
Fast LD computation from VCF files using tomahawk
ld
snp
vcf
vcftools
bcftools
updated 13 months ago by
Ram
43k • written 5.5 years ago by
firestar
★ 1.6k
15
votes
4
replies
4.6k
views
Tutorial:
RNASeq tutorial for gene differential expression analysis
Transcriptomics
bioconductor
RNA-Seq
R
updated 13 months ago by
Ram
43k • written 3.7 years ago by
Thind amarinder
▴ 340
0
votes
4
replies
726
views
Tutorial:
Reverse pharmacology: how to predict drugs with genes or disease names?
drugs
drug-targets
genes
5 months ago by
Coremine Medical
▴ 20
20
votes
4
replies
2.6k
views
Tutorial:
Bash One-liners collection on Github
bash
linux
shell
updated 13 months ago by
Ram
43k • written 5.0 years ago by
nim.1111.ou
▴ 180
12
votes
4
replies
2.2k
views
Tutorial:
Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR
DESeq2
updated 13 months ago by
Ram
43k • written 6.6 years ago by
KVC_bioinfo
▴ 590
19
votes
4
replies
8.9k
views
Tutorial:
Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 14 months ago by
Ram
43k • written 11.1 years ago by
Istvan Albert
100k
10
votes
4
replies
11k
views
Tutorial:
Using the MinION MinKNOW software on Ubuntu 1604
long-reads
oxford-nanopore
minion
updated 13 months ago by
Ram
43k • written 4.8 years ago by
colindaven
6.4k
20
votes
4
replies
8.6k
views
Tutorial:
DE analysis by edgeR
RNA-Seq
R
edgeR
updated 12 months ago by
Ram
43k • written 7.6 years ago by
zizigolu
★ 4.3k
24
votes
4
replies
7.7k
views
Tutorial:
Using EnrichedHeatmap for visualization of NGS experiments
heatmap
chip-seq
atac-seq
EnrichedHeatmap
updated 13 months ago by
Ram
43k • written 4.7 years ago by
ATpoint
82k
6
votes
4
replies
7.5k
views
Tutorial:
Overlay Multiple Tracks In Ucsc Browser [Quick Minimal Tutorial]
visualization
ChIP-seq
RNA-seq
ucsc-genome-browser
bigwig
updated 14 months ago by
Ram
43k • written 11.1 years ago by
Sukhi Singh
11k
8
votes
3
replies
2.8k
views
Tutorial:
Free online interactive Ensembl training
ensembl
training
genome
updated 21 months ago by
Ram
43k • written 8.2 years ago by
Emily
23k
11
votes
3
replies
1.4k
views
Tutorial:
Creating great documentation for bioinformatics software
Software-Documentation
updated 12 months ago by
Ram
43k • written 7.8 years ago by
venu
7.1k
3
votes
3
replies
2.8k
views
Tutorial:
Generating count matrix for STAR counts in GDC v32.0 for RNA-Seq
GDC
TCGABiolinks
STAR
updated 14 months ago by
Ram
43k • written 2.0 years ago by
DareDevil
★ 4.3k
10
votes
3
replies
4.5k
views
Tutorial:
Video: Alternative Splicing and Primer Design
RNA-Seq
IGB
updated 15 months ago by
Ram
43k • written 9.6 years ago by
Nowlan Freese
▴ 860
3
votes
3
replies
8.8k
views
Tutorial:
High Speed Downloading of SRA, SAM and Fastq Files
fastq
sam
Aspera-Connect
sra
updated 11 months ago by
Ram
43k • written 6.3 years ago by
Wenhu_Cao
▴ 100
6
votes
3
replies
4.5k
views
Tutorial:
Principles and Workflow of 16S/18S/ITS Amplicon Sequencing
alignment
sequencing
RNA-seq
gene
updated 13 months ago by
Ram
43k • written 5.5 years ago by
contact
▴ 40
14
votes
3
replies
20k
views
Tutorial:
Plotting the coverage and depth (Y-axis) statistics of a bam file along the genome (X-axis), using Samtools, awk and R.
genome
plot
coverage
samtools
updated 8 months ago by
William
▴ 30 • written 7.1 years ago by
kirannbishwa01
★ 1.6k
2
votes
3
replies
216
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 1 hour ago by
Ram
43k • written 1 day ago by
Ming Tommy Tang
★ 3.9k
411 results • Page
3 of 9
Recent Votes
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Answer: Trimming tools - your experience please?
Comment: PCA plot
C: RNA seq library size
RNA seq library size
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
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chaco001
▴ 40
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to
GenoMax
141k
Popular Question
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rheab1230
▴ 140
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BioinfGuru
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Recent Replies
Comment: Heatmap and rna-seq
by
GenoMax
141k
Please include a link when you are recommending a tool. There can be programs with similar names.
Answer: Heatmap and rna-seq
by
dsull
★ 5.8k
Check out clustergrammer from Avi Ma'ayan's lab.
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Simple: ```r data <- lapply(files, read_tsv) data <- Reduce(merge, data) # or Reduce(full_join, data) ``` <a href="" title="Text added bec…
Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
by
ATpoint
82k
You can make each process use a dedicated environment, see https://www.nextflow.io/docs/latest/conda.html#use-existing-conda-environments …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Hi, Just thought I'd share this code snippet here for when each file contains multiple samples. I tried using lapply (as suggested by Ram)…
Comment: Low mapping rate with Salmon
by
i.sudbery
19k
Take your STAR alignment and sum all the counts for each gene. You can either do this by providing an annotation to STAR, or by running fea…
Comment: How to convert plink files to Hapmap Format
by
bk11
★ 2.4k
If you run your data with plink 2.0, you will have ERRCODE column in your result file showing the reason behind "NA" p-value. https://www.b…
Comment: genome assembly records not present in assembly_summary.txt
by
sapuizait
▴ 10
jesus its in the Genbank file and I was looking at the refseq! I m such a moron - thanks for pointing it out -sorry about that :(
Comment: ScRNA data question
by
bk11
★ 2.4k
I wonder how the `Vlnplots` will look if you normalize the data using `NormalizeData()` function in `Seurat`. The flat line in your plot ar…
Comment: Low mapping rate with Salmon
by
GenoMax
141k
> Does that mean that the reads that are not mapped to my trascriptome are not exons/coding genes? Reads are likely aligning in regions wh…
Comment: How Can We Find The Info For 3'Utr And 5'Utr In Gencode Gtf File?
by
cmdcolin
★ 3.8k
the gencode link is broken now but here is a back up of that blogpost on archive https://web.archive.org/web/20130618221342/http://gencodeg…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
I'll try to make the decoy file again but I remember you also told me that it is only recommended and not mandatory for running `salmon`. I…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
For doing this, should I just look at the log.out.file?
Answer: Heatmap and rna-seq
by
pinheirofabiano
▴ 10
install.packages("pheatmap") library(pheatmap) setwd("/Users/data_analysis/results") data <- read.table(file…
Comment: Low mapping rate with Salmon
by
Patadu94
• 0
Thanks for the link GenoMax. But I was wondering, should not alignment and mapping have a similar rate and thus be correlated? In my case I…
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