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412 results • Page 3 of 9
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Tutorial: CorLevelPlot - Visualise correlation results, e.g., clinical parameter correlations
correlation corlevelplot
updated 7 weeks ago by 43k • written 6.2 years ago by 88k
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 22 months ago by 43k • written 8.3 years ago by ★ 4.3k
46
votes
6
replies
25k
views
Tutorial: Greatly speed up conda by using mamba
software
updated 2.3 years ago by ▴ 50 • written 3.1 years ago by 13k
43
votes
6
replies
12k
views
Tutorial: Annotating TCGA MAFs with the latest Ensembl/Gencode transcripts
ensembl maf tcga vcf
updated 14 months ago by 43k • written 10.3 years ago by 6.1k
67
votes
6
replies
26k
views
7 follow
Tutorial: Rna-Seq Review Papers
RNA-seq papers
updated 14 months ago by 43k • written 11.7 years ago by 100k
61
votes
6
replies
9.5k
views
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 14 months ago by 43k • written 10.8 years ago by 9.7k
13
votes
6
replies
6.0k
views
Tutorial: Trim & align paired-end reads in a single pass
align trim fastq pipe paired-end
updated 13 months ago by 43k • written 7.9 years ago by 14k
106
votes
6
replies
26k
views
6 follow
Tutorial: Creating workflows with snakemake and conda
workflow snakemake conda
updated 14 months ago by 43k • written 5.7 years ago by 16k
70
votes
5
replies
11k
views
8 follow
Tutorial: Bioinformatics For Metagenomic Analyses
QC taxonomy metagenomics
updated 2.1 years ago by 43k • written 10.1 years ago by ★ 1.8k
16
votes
5
replies
9.0k
views
Tutorial: Using The Biomart Perl Api For Simple Queries
api perl biomart
updated 14 months ago by 43k • written 11.7 years ago by 20k
5
votes
5
replies
663
views
Tutorial: how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix RNAseq R
updated 13 days ago by • 0 • written 22 days ago by ★ 3.9k
6
votes
5
replies
7.0k
views
Tutorial: use firehose_get to download TCGA data
tcga RNA-Seq
updated 12 months ago by 43k • written 6.5 years ago by ▴ 140
2
votes
5
replies
2.2k
views
Tutorial: Building OMA database on SGE
oma
updated 13 months ago by 43k • written 7.9 years ago by ▴ 10
10
votes
5
replies
24k
views
Tutorial: Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 14 months ago by 43k • written 5.8 years ago by ★ 9.4k
64
votes
5
replies
7.3k
views
10 follow
Tutorial: Informatics of RNA-Seq.
next-gen RNA-Seq
updated 19 months ago by 43k • written 8.8 years ago by 12k
15
votes
5
replies
16k
views
Tutorial: How to create a mutation lolliplot with GenVisR
bioconductor graphics R genvisr
updated 13 months ago by 43k • written 7.9 years ago by 20k
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 43k • written 10.5 years ago by ★ 1.2k
12
votes
5
replies
8.4k
views
Tutorial: How To Install BioPerl Without Root Privileges in Ubuntu/Linxu
bioperl
updated 13 months ago by 43k • written 8.0 years ago by ★ 9.4k
29
votes
5
replies
6.4k
views
Tutorial: Gnu Parallel Tutorial
parallel gnu-parallel
updated 14 months ago by 43k • written 10.7 years ago by ★ 4.4k
21
votes
5
replies
6.8k
views
Tutorial: Analysis of single-cell RNA-seq data
single-cell RNA-Seq
updated 13 months ago by 43k • written 7.9 years ago by ★ 1.5k
1
vote
5
replies
664
views
Tutorial: Single-cell RNA-seq: Annotation: Celltype annotation migration(mapping) with TOSICA
scRNA-seq TOSICA
updated 3 months ago by 43k • written 4 months ago by ▴ 120
16
votes
5
replies
13k
views
6 follow
Tutorial: Easy way to do GO enrichment in R
enrichr RNA-Seq gene R
updated 14 months ago by 43k • written 6.5 years ago by ▴ 800
12
votes
5
replies
2.5k
views
Tutorial: FASTA file split
fasta
updated 14 months ago by 43k • written 3.9 years ago by 8.6k
9
votes
5
replies
2.3k
views
Tutorial: What is new in samtools release 1.5 [Solstice Release] (21st June 2017)
samtools
updated 12 months ago by 43k • written 6.8 years ago by 100k
37
votes
5
replies
6.1k
views
Tutorial: [Beginner] Introduction to bioinformatics file types
fastq fasta bed SAM
updated 8 months ago by ▴ 20 • written 8.8 years ago by ▴ 430
15
votes
4
replies
4.6k
views
Tutorial: RNASeq tutorial for gene differential expression analysis
Transcriptomics bioconductor RNA-Seq R
updated 14 months ago by 43k • written 3.8 years ago by ▴ 340
1
vote
4
replies
3.4k
views
Tutorial: Applying machine learning to NGS transcriptomic data
next-gen RNA-Seq
updated 12 months ago by 43k • written 6.0 years ago by ▴ 340
32
votes
4
replies
8.0k
views
Tutorial: Fast LD computation from VCF files using tomahawk
ld snp vcf vcftools bcftools
updated 14 months ago by 43k • written 5.5 years ago by ★ 1.6k
24
votes
4
replies
7.7k
views
Tutorial: Using EnrichedHeatmap for visualization of NGS experiments
heatmap chip-seq atac-seq EnrichedHeatmap
updated 14 months ago by 43k • written 4.8 years ago by 82k
12
votes
4
replies
5.4k
views
Tutorial: *FREE course* Bioinformatics for Biologists: An Introduction to Linux, Bash Scripting, and R
linux R
updated 15 months ago by 43k • written 3.3 years ago by ▴ 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 12 months ago by 43k • written 6.0 years ago by ★ 2.5k
0
votes
4
replies
773
views
Tutorial: Reverse pharmacology: how to predict drugs with genes or disease names?
drugs drug-targets genes
6 months ago by Coremine Medical ▴ 20
10
votes
4
replies
5.7k
views
Tutorial: Unsupervised clustering on gene expression data
gene-expression clustering RNA-seq
9 months ago by Hamid Ghaedi 3.2k
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 43k • written 11.2 years ago by 20k
1
vote
4
replies
3.5k
views
Tutorial: How to install C++ compilers/make from GNU for Gromacs?
Gromacs Cpp-compilers GNU
updated 13 months ago by 43k • written 7.9 years ago by ▴ 10
20
votes
4
replies
8.6k
views
Tutorial: DE analysis by edgeR
RNA-Seq R edgeR
updated 13 months ago by 43k • written 7.7 years ago by ★ 4.3k
19
votes
4
replies
8.9k
views
Tutorial: Rna Seq Experimental Design For Measuring Differential Gene Expression
RNA-seq
updated 14 months ago by 43k • written 11.2 years ago by 100k
10
votes
4
replies
11k
views
Tutorial: Using the MinION MinKNOW software on Ubuntu 1604
long-reads oxford-nanopore minion
updated 14 months ago by 43k • written 4.9 years ago by 6.4k
3
votes
4
replies
3.6k
views
Tutorial: Gene Set Enrichment Analysis on T-BioInfo
gene RNA-Seq
updated 11 months ago by 43k • written 5.6 years ago by ▴ 340
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 43k • written 11.2 years ago by 11k
12
votes
4
replies
2.2k
views
Tutorial: Tutorials for Library Normalization in DESeq2 and EdgeR
EdgeR DESeq2
updated 14 months ago by 43k • written 6.7 years ago by ▴ 590
20
votes
4
replies
2.7k
views
Tutorial: Bash One-liners collection on Github
bash linux shell
updated 14 months ago by 43k • written 5.0 years ago by ▴ 180
29
votes
4
replies
4.5k
views
Tutorial: Modern Statistics for Modern Biology
statistics
updated 14 months ago by 43k • written 5.3 years ago by 27k
3
votes
3
replies
8.8k
views
Tutorial: High Speed Downloading of SRA, SAM and Fastq Files
fastq sam Aspera-Connect sra
updated 12 months ago by 43k • written 6.4 years ago by ▴ 100
4
votes
3
replies
4.6k
views
Tutorial: How to get full taxonomy classification using taxize and myTAI
taxonomy R
updated 14 months ago by 43k • written 6.1 years ago by ★ 4.0k
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 9 months ago by ▴ 30 • written 7.1 years ago by ★ 1.6k
2
votes
3
replies
645
views
Tutorial: Bulk RNA-seq: Different Expression Analysis with DEseq2
python pyDESeq2 RNA-seq
updated 4 months ago by 43k • written 4 months ago by ▴ 120
13
votes
3
replies
5.1k
views
Tutorial: Video: Visualization of whole genome DNA methylation data in IGB
Bismark BS-Seq RNA-Seq IGB
updated 24 months ago by 43k • written 9.2 years ago by ▴ 860
11
votes
3
replies
1.4k
views
Tutorial: Creating great documentation for bioinformatics software
Software-Documentation
updated 13 months ago by 43k • written 7.8 years ago by 7.1k
9
votes
3
replies
4.2k
views
Tutorial: Ht Sequence Analysis With R And Bioconductor By The Bioinformatics Center At Uc Riverside
bioconductor
updated 15 months ago by 43k • written 11.7 years ago by 100k
412 results • Page 3 of 9
Recent Votes
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences?
Answer: Details on salmon index
Comment: zero TPM for many gene including housekeeping when using kallisto
Sequence Alignment from Scratch with BWA
Answer: mitochondrial genome assembly pipeline
Comment: Help! Reconstruction of locus, order contigs
Comment: In one PCA plot, can I calculate the percentage of different factors that contri
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Recent Replies
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
I don't understand your comment. What do you mean? > my idea is not to have to write it down If you have an alignment already, why can't…
Comment: Help! Reconstruction of locus, order contigs by GenoMax 142k
Please use `ADD REPLY/ADD COMMENT` when responding to existing content. `SUBMIT ANSWER` is for new answers to the original question.
Comment: Details on salmon index by Rob 6.6k
Hi Lorenzo, That is correct. The initial version of salmon used the RapMap index explained above. When we published the selective align…
Comment: Help! Reconstruction of locus, order contigs by BATMAN • 0
Thanks for your reply, my idea is not to have to write it down. What I have is an alignment of the .gbk from the progressiveMauve. It would…
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
I did some digging aroumd, no static binary. Plus it seems you need to roll your own program.
Comment: Faster Needleman-Wunsch rapid global alignment of two sequences? by Gabriel R. ★ 2.9k
We tested it, however, it does not seem to produce a fast a file of the results or anything that we can easily parse. It produces a CIGAR a…
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint yes but for example for the kallisto results I have expression for 2080 genes (transcripts) and the rest are 0 but in my STAR resu…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by marco.barr ▴ 130
great team work! why can't you access and do the calculation for the other components too? can't you extract the information from the other…
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Yes, but this is what I am saying: GAPDH in human has at least 6 annotated transcripts. Have you looked at all of them? Maybe that particul…
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint these are from PBMC. no they are different genes. for example ENST00000229239.10 is GAPDH. in STAR I got a lot of reads aligned …
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@dariober: I have to use kallisto for our downstream pipeline.
Comment: zero TPM for many gene including housekeeping when using kallisto by ATpoint 82k
Which celltype is this? Are these transcripts of the same gene, and of which gene?
Comment: zero TPM for many gene including housekeeping when using kallisto by ashkan ▴ 160
@atpoint the question is updated. the first command shows how the index is built.
Comment: Help! Reconstruction of locus, order contigs by dthorbur ★ 2.0k
Is the *de novo* annotation required for each contig? Reconstructing homologous regions in many genomes can be tricky regardless, but is es…
Comment: In one PCA plot, can I calculate the percentage of different factors that contri by diqixiaoyaoer ▴ 20
You can have a look on my answer. I have post it below.
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