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352 results • Page
1 of 8
Sort: Votes
Rank
Views
Votes
Replies
276
votes
39
replies
164k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
download
GEO
bam
updated 10 months ago by
Ram
38k • written 8.6 years ago by
Obi Griffith
20k
274
votes
33
replies
91k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 21 days ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
238
votes
176
replies
84k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 5 months ago by
Ram
38k • written 7.6 years ago by
TriS
★ 4.6k
194
votes
44
replies
68k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 10 weeks ago by
Ram
38k • written 10.5 years ago by
Obi Griffith
20k
146
votes
35
replies
58k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 26 days ago by
Ram
38k • written 10.3 years ago by
vijay
★ 1.6k
145
votes
34
replies
51k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 25 days ago by
Ram
38k • written 9.9 years ago by
Cyriac Kandoth
5.9k
144
votes
68
replies
43k
views
18 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 8 days ago by
Ram
38k • written 5.3 years ago by
Kevin Blighe
84k
142
votes
21
replies
29k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 10 months ago by
Ram
38k • written 8.3 years ago by
Parham
★ 1.6k
136
votes
25
replies
75k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 11 months ago by
Ram
38k • written 10.9 years ago by
Ying W
★ 4.2k
130
votes
122
replies
28k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 12 days ago by
Ram
38k • written 4.4 years ago by
Kevin Blighe
84k
116
votes
66
replies
40k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 8 days ago by
Ram
38k • written 4.7 years ago by
ATpoint
70k
99
votes
16
replies
30k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 7 days ago by
Ram
38k • written 6.6 years ago by
Jean-Karim Heriche
26k
99
votes
8
replies
27k
views
8 follow
Tutorial:
Guide to TCGA data
TCGA
cancer
tools
RNA-Seq
clinical
Tutorial
updated 6.3 years ago by
ewre
▴ 250 • written 7.1 years ago by
Jordan Anaya
★ 1.1k
98
votes
6
replies
22k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 7 days ago by
Ram
38k • written 4.5 years ago by
finswimmer
16k
94
votes
25
replies
31k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 27 days ago by
Ram
38k • written 10.5 years ago by
Istvan Albert
96k
92
votes
105
replies
34k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 8 days ago by
Ram
38k • written 4.6 years ago by
Kevin Blighe
84k
89
votes
19
replies
30k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 20 days ago by
Ram
38k • written 9.4 years ago by
Obi Griffith
20k
83
votes
34
replies
15k
views
21 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
active-subnetwork
enrichment
pathway
R
updated 12 days ago by
Ram
38k • written 4.7 years ago by
egeulgen
★ 1.3k
82
votes
28
replies
28k
views
19 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 5 weeks ago by
Ram
38k • written 7.0 years ago by
Obi Griffith
20k
81
votes
8
replies
7.8k
views
6 follow
Tutorial:
Current Topics in Genome Analysis 2014 (collection of educational lectures)
workshop
lectures
genomics
training
updated 15 days ago by
Ram
38k • written 8.8 years ago by
Malachi Griffith
19k
81
votes
21
replies
70k
views
13 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 4 weeks ago by
cmdcolin
★ 2.9k • written 4.7 years ago by
otwtgin2010
▴ 530
81
votes
21
replies
14k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 12 days ago by
Ram
38k • written 2.4 years ago by
Hamid Ghaedi
2.9k
79
votes
2
replies
53k
views
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 22 days ago by
Ram
38k • written 9.7 years ago by
Eric Normandeau
11k
78
votes
41
replies
28k
views
24 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 3 months ago by
Acadia
• 0 • written 9.4 years ago by
Irsan
★ 7.7k
76
votes
13
replies
14k
views
12 follow
Tutorial:
Exploring cancer mutation data portals
TCGA
Cancer
ICGC
Data-Portal
Mutation
updated 17 months ago by
Ram
38k • written 8.8 years ago by
Malachi Griffith
19k
75
votes
70
replies
16k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 7 days ago by
Ram
38k • written 5.1 years ago by
Kevin Blighe
84k
74
votes
13
replies
65k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 4 months ago by
Ram
38k • written 9.3 years ago by
Nicholas Spies
★ 1.2k
73
votes
14
replies
14k
views
15 follow
Tutorial:
List Of Bioinformatics Books
books
updated 5 weeks ago by
Ram
38k • written 9.8 years ago by
Medhat
9.5k
72
votes
48
replies
15k
views
15 follow
Tutorial:
For Short Reads, Which Aligners Find All Hits Given Certain Edit Distance Threshold?
ngs
alignment
bwa
updated 26 days ago by
Ram
38k • written 10.1 years ago by
lh3
33k
72
votes
60
replies
23k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 5 weeks ago by
Ram
38k • written 5.5 years ago by
Kevin Blighe
84k
70
votes
5
replies
10k
views
8 follow
Tutorial:
Bioinformatics For Metagenomic Analyses
QC
taxonomy
metagenomics
updated 11 months ago by
Ram
38k • written 9.0 years ago by
umer.zeeshan.ijaz
★ 1.8k
69
votes
3
replies
34k
views
Tutorial:
Revisiting the FastQC read duplication report
fastqc
updated 16 months ago by
Ram
38k • written 8.7 years ago by
Istvan Albert
96k
68
votes
26
replies
24k
views
15 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 19 days ago by
Ram
38k • written 9.1 years ago by
Istvan Albert
96k
67
votes
6
replies
24k
views
7 follow
Tutorial:
Rna-Seq Review Papers
RNA-seq
papers
updated 27 days ago by
Ram
38k • written 10.6 years ago by
Istvan Albert
96k
65
votes
9
replies
47k
views
7 follow
Tutorial:
Reference Assembly - Mapping Reads To A Reference Genome
reference
samtools
mapping
bwa
updated 6 weeks ago by
Ram
38k • written 9.7 years ago by
Joseph Hughes
★ 3.0k
64
votes
26
replies
11k
views
11 follow
Tutorial:
Generating consensus sequence from bam file
fasta
consensus
bam
updated 8 days ago by
Ram
38k • written 4.0 years ago by
finswimmer
16k
64
votes
5
replies
6.7k
views
10 follow
Tutorial:
Informatics of RNA-Seq.
next-gen
RNA-Seq
updated 5 months ago by
Ram
38k • written 7.6 years ago by
GouthamAtla
12k
64
votes
26
replies
11k
views
7 follow
Tutorial:
Parallel processing in R
biocparallel
mclapply
foreach
R
updated 7 days ago by
Ram
38k • written 5.5 years ago by
Kevin Blighe
84k
63
votes
13
replies
12k
views
11 follow
Tutorial:
Tutorial (How to analyze) on Whole Exome sequencing. Common Errors. Best Practices.
muTect
GATK
Picard
Exome
updated 13 months ago by
Ram
38k • written 8.4 years ago by
Chirag Nepal
★ 2.3k
60
votes
6
replies
8.9k
views
Tutorial:
Minimum Standards For Bioinformatics Command Line Tools
command-line
updated 22 days ago by
Ram
38k • written 9.6 years ago by
Medhat
9.5k
60
votes
52
replies
39k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 7 days ago by
Ram
38k • written 6.5 years ago by
steve
★ 3.3k
60
votes
2
replies
6.9k
views
Tutorial:
Table Of Contents To All Review Paper Compilations On Biostar
papers
updated 27 days ago by
Ram
38k • written 10.6 years ago by
Istvan Albert
96k
59
votes
43
replies
18k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 7 days ago by
Ram
38k • written 5.5 years ago by
Rox
★ 1.4k
59
votes
15
replies
11k
views
Tutorial:
Which human reference genome should I use?
genome
alignment
assembly
Tutorial
4.4 years ago by
finswimmer
16k
58
votes
25
replies
36k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 4 days ago by
Ram
38k • written 6.6 years ago by
Shicheng Guo
★ 9.3k
53
votes
5
replies
14k
views
6 follow
Tutorial:
Machine Learning For Cancer Classification - Part 4 - Plotting A Kaplan-Meier Curve For Survival Analysis
r
updated 5 months ago by
Ram
38k • written 9.3 years ago by
Nicholas Spies
★ 1.2k
51
votes
3
replies
22k
views
Tutorial:
Sam File Format - Lesser Known Tips And Tricks
sam
updated 26 days ago by
Ram
38k • written 10.2 years ago by
Ya
▴ 300
51
votes
19
replies
41k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 29 days ago by
Ram
38k • written 10.9 years ago by
Sukhi Singh
11k
50
votes
3
replies
4.0k
views
Tutorial:
[[ Please read before posting a question ::: How To Ask A Good Question ]]
how-to
updated 7 days ago by
Ram
38k • written 4.2 years ago by
ATpoint
70k
48
votes
7
replies
11k
views
7 follow
Tutorial:
Genome Assembly Review Papers
assembly
papers
updated 27 days ago by
Ram
38k • written 10.6 years ago by
Istvan Albert
96k
352 results • Page
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Recent Votes
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Comment: Snakemake vs Nextflow Upcoming bioinformatics Project
Comment: Snakemake vs Nextflow Upcoming bioinformatics Project
Answer: Creating a loop to mark duplicates using Picard
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Comment: advice on course selection for a bioinformatics career.
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
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Comment: Creating loop for read groups using Picard
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duplicate of https://www.biostars.org/p/9558127/
Comment: ClusterProfiler enrichKEGG – remove organism name in plots?
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Is there a problem in using program version that produced your top plot? Unless there is known bug in a program, or a super-useful feature…
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Not in one step that I could find, but this works: deletions: ``` bcftools view --types indels --include 'ILEN<0' file.vcf | bcftools …
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Thank you, sir. I have looked into your thesis. It's really great. I may have a try on Gviz if I don't have any idea about my question.
Comment: Snakemake vs Nextflow Upcoming bioinformatics Project
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Brilliant, thanks for the advice, i think after looking into what the community has said I have invested into learning the groovy language …
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
by
Juke34
7.7k
Change merge_loci to true
Comment: msigdbr returns the same genesets for mouse as in for human,
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The addition of mouse-specific pathways to MSigDB is relatively recent. The package has not been updated to incorporate the latest version …
Comment: known-sites for Felis_catus_9.0 (GCA_000181335.4)
by
makarov
• 0
Thank you, I also found vcf files https://ftp.ensembl.org/pub/release-109/variation/vcf/felis_catus/
Comment: Creating a loop to mark duplicates using Picard
by
Ram
38k
For someone new at shell scripts, you're doing really well at using shell variables and parameter expansion. Good going!
Comment: Creating a loop to mark duplicates using Picard
by
brandnewatthis
• 0
Sorry, I am very new at this and am just learning my way around these symbols! Thanks for the help :)
Comment: How can I easily remove overlapping transcripts, keeping only longest transcript
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BioinfoBee
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its version 1.0.0. and installed using conda. How do I configure config.yaml file in such case?
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> Can I Yes. Should you? Probably not. There must be better, statistically more robust ways of quantifying based on biological replicates.
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You should be able to do `fasterq-dump <SRR number> -O output_folder`
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If you are trying to re-create an analysis and if it used both SRA# then you will need to get both. If you are simply learning/testing then…
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