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412 results • Page
1 of 9
Sort: Views
Rank
Views
Votes
Replies
288
votes
39
replies
184k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 13 months ago by
Ram
43k • written 9.7 years ago by
Obi Griffith
20k
298
votes
33
replies
109k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 14 months ago by
Ram
43k • written 10.6 years ago by
Obi Griffith
20k
239
votes
176
replies
96k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 11 months ago by
Ram
43k • written 8.8 years ago by
TriS
★ 4.7k
55
votes
14
replies
93k
views
10 follow
Tutorial:
Using R in Conda
R
updated 14 months ago by
Ram
43k • written 3.8 years ago by
rohitsatyam102
▴ 860
93
votes
23
replies
93k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 3 months ago by
clara.apicella
• 0 • written 5.8 years ago by
otwtgin2010
▴ 610
139
votes
25
replies
84k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 2.1 years ago by
Ram
43k • written 12.1 years ago by
Ying W
★ 4.2k
30
votes
10
replies
82k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 14 months ago by
Ram
43k • written 3.2 years ago by
Nitin Narwade
★ 1.6k
196
votes
44
replies
72k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 16 months ago by
Ram
43k • written 11.6 years ago by
Obi Griffith
20k
75
votes
13
replies
67k
views
10 follow
Tutorial:
Machine Learning For Prediction of Relapse in Cancer - Part 2 - Building A Random Forest Classifier
r
cancer
classification
updated 18 months ago by
Ram
43k • written 10.5 years ago by
Nicholas Spies
★ 1.2k
149
votes
35
replies
62k
views
33 follow
Tutorial:
Tools For Metagenomic Data Analysis
metagenomics
next-gen
updated 14 months ago by
Ram
43k • written 11.5 years ago by
vijay
★ 1.6k
2
votes
1
reply
61k
views
Tutorial:
Docker denied: requested access to the resource is denied
docker
updated 22 months ago by
LauferVA
4.2k • written 22 months ago by
kodwings
▴ 20
87
votes
2
replies
59k
views
6 follow
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 14 months ago by
Ram
43k • written 10.9 years ago by
Eric Normandeau
11k
147
votes
34
replies
55k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 14 months ago by
Ram
43k • written 11.1 years ago by
Cyriac Kandoth
6.1k
0
votes
3
replies
53k
views
Tutorial:
Installation VMD on LINUX_64
gromacs
VMD
updated 13 months ago by
Ram
43k • written 7.9 years ago by
Hassan Rasouli
▴ 10
150
votes
70
replies
51k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 8 months ago by
Raheleh
▴ 260 • written 6.5 years ago by
Kevin Blighe
88k
66
votes
9
replies
49k
views
7 follow
Tutorial:
Reference Assembly - Mapping Reads To A Reference Genome
reference
samtools
mapping
bwa
updated 15 months ago by
Ram
43k • written 10.9 years ago by
Joseph Hughes
★ 3.0k
100
votes
106
replies
47k
views
26 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 5 weeks ago by
psb7
▴ 20 • written 5.7 years ago by
Kevin Blighe
88k
117
votes
66
replies
46k
views
20 follow
Tutorial:
[Deprecated] Fast download of FASTQ files from the European Nucleotide Archive (ENA)
aspera
fastq-dump
Fastq
ENA
updated 14 months ago by
Ram
43k • written 5.9 years ago by
ATpoint
82k
60
votes
52
replies
44k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 14 months ago by
Ram
43k • written 7.6 years ago by
steve
★ 3.5k
53
votes
19
replies
44k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 14 months ago by
Ram
43k • written 12.1 years ago by
Sukhi Singh
11k
58
votes
25
replies
40k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 14 months ago by
Ram
43k • written 7.8 years ago by
Shicheng Guo
★ 9.4k
75
votes
3
replies
39k
views
Tutorial:
Revisiting the FastQC read duplication report
fastqc
updated 2.5 years ago by
Ram
43k • written 9.8 years ago by
Istvan Albert
100k
133
votes
123
replies
38k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 13 months ago by
1769mkc
★ 1.2k • written 5.6 years ago by
Kevin Blighe
88k
39
votes
16
replies
37k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 4 months ago by
GenoMax
142k • written 3.7 years ago by
lavinia.gordon
▴ 160
45
votes
2
replies
37k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 15 months ago by
Ram
43k • written 12.1 years ago by
MSU course 2011
▴ 540
99
votes
16
replies
34k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 14 months ago by
Ram
43k • written 7.8 years ago by
Jean-Karim Heriche
27k
90
votes
48
replies
34k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 6 months ago by
Ram
43k • written 10.6 years ago by
Irsan
★ 7.8k
95
votes
25
replies
33k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 14 months ago by
Ram
43k • written 11.6 years ago by
Istvan Albert
100k
90
votes
19
replies
32k
views
12 follow
Tutorial:
Machine Learning For Cancer Classification - Part 1 - Preparing The Data Sets
microarray
bioconductor
expression
classification
updated 14 months ago by
Ram
43k • written 10.5 years ago by
Obi Griffith
20k
84
votes
29
replies
32k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 9 months ago by
amziepickles
• 0 • written 8.2 years ago by
Obi Griffith
20k
34
votes
12
replies
30k
views
7 follow
Tutorial:
So What Does The Sequence Duplication Rate Really Mean In A Fastqc Report
quality-control
fastqc
updated 14 months ago by
Ram
43k • written 10.6 years ago by
Istvan Albert
100k
142
votes
21
replies
30k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 2.0 years ago by
Ram
43k • written 9.4 years ago by
Parham
★ 1.6k
99
votes
8
replies
29k
views
8 follow
Tutorial:
Guide to TCGA data
cancer
RNA-Seq
clinical
TCGA
updated 13 months ago by
Ram
43k • written 8.2 years ago by
Jordan Anaya
★ 1.1k
73
votes
27
replies
28k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 5 months ago by
snardeli
• 0 • written 10.3 years ago by
Istvan Albert
100k
73
votes
60
replies
28k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 15 months ago by
Ram
43k • written 6.7 years ago by
Kevin Blighe
88k
106
votes
6
replies
26k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 14 months ago by
Ram
43k • written 5.7 years ago by
finswimmer
16k
67
votes
6
replies
26k
views
7 follow
Tutorial:
Rna-Seq Review Papers
RNA-seq
papers
updated 14 months ago by
Ram
43k • written 11.7 years ago by
Istvan Albert
100k
46
votes
6
replies
25k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 2.3 years ago by
cameron.cowan
▴ 50 • written 3.1 years ago by
rpolicastro
13k
10
votes
5
replies
24k
views
Tutorial:
Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 14 months ago by
Ram
43k • written 5.8 years ago by
Shicheng Guo
★ 9.4k
42
votes
16
replies
24k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 21 months ago by
Ram
43k • written 8.7 years ago by
Chirag Nepal
★ 2.4k
87
votes
24
replies
23k
views
17 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 27 days ago by
Gordon
• 0 • written 3.6 years ago by
Hamid Ghaedi
3.2k
51
votes
3
replies
23k
views
Tutorial:
Sam File Format - Lesser Known Tips And Tricks
sam
updated 14 months ago by
Ram
43k • written 11.3 years ago by
Ya
▴ 300
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
59
votes
43
replies
21k
views
18 follow
Tutorial:
Polish PacBio assembly with latest PacBio tools : an affordable solution for everyone
pbalign
pacbio
arrow
smrt-limk
updated 14 months ago by
Ram
43k • written 6.7 years ago by
Rox
★ 1.4k
34
votes
16
replies
20k
views
14 follow
Tutorial:
TCGA UUIDS to TCGA barcode (SampleID) in R
next-gen
GDC
R
TCGA
updated 8 weeks ago by
aUser
▴ 30 • written 7.6 years ago by
martinguerrerog89
▴ 310
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
William
▴ 30 • written 7.1 years ago by
kirannbishwa01
★ 1.6k
76
votes
72
replies
20k
views
19 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
20 days ago by
Kevin Blighe
88k
39
votes
6
replies
20k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 12 months ago by
Ram
43k • written 6.7 years ago by
steve
★ 3.5k
83
votes
34
replies
19k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 11 months ago by
adelheidkratzer
• 0 • written 5.9 years ago by
egeulgen
★ 1.3k
18
votes
40
replies
18k
views
16 follow
Tutorial:
Easy way to run easily orthoMCL (Copy & paste)
all-v-all
orthomcl
updated 3.9 years ago by
krishdb38
• 0 • written 7.9 years ago by
Esaie
▴ 170
412 results • Page
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Recent Votes
Comment: Overlapping Ranges within Granges object
Answer: Difference between Genotype 0|1 and 1|0 in VCF file?
Answer: how to keep reads in a fasta file based on a seq id list in R?
Answer: The total expressed genes in RNA-Seq data
C: Re-arrange conditions in Seurat
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Answer: Genome Visualization Tools
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Comment: Overlapping Ranges within Granges object
by
ntsopoul
▴ 60
you are on to something… if I use reduce to find the “overlaping regions” in a secon GRanges object, what do I do next?
Comment: Using ggplotly in R
by
jen
▴ 10
Thank you Jared for your response. I took a look at the documentation you provided and am trying my best to follow along, but can't seem to…
Comment: Getting the coding_sequence.fasta from the .gff file from the AUGUSTUS gene pred
by
Juke34
8.6k
Right I heard there is an issue since Perl v5.36. You may have better luck using conda. Or the best way is to use the container. Or downgra…
Answer: Alphaphold 3 pLDDT coloring scheme in chimerax?
by
Mensur Dlakic
★ 27k
pLDDT scores are stored in the so-called B-factor column in PDB files. Below the `File` ribbon select `Molecule Display` and click on `b-fa…
Comment: Genome Visualization Tools
by
dlera.lozano
▴ 10
Thank you so much
Answer: Doubt about the process of annotation, detection, identification and classificat
by
Mensur Dlakic
★ 27k
Depends on the context. `TE detection` and `TE identification` could mean the same thing if they refer to presence/absence of TEs. `TE iden…
Comment: featureCounts output summary assigned value higher than uniquely mapped reads fr
by
Ram
43k
Please accept your own answer to mark the post as solved.
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Ram
43k
A small educational note: if an answer was helpful, you should upvote it; if the answer resolved your question, you should mark it as accep…
Comment: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Prawesh
• 0
thanks, it's working now.
Answer: Genome Visualization Tools
by
GenoMax
142k
@cmdcolin has a great list here: https://github.com/cmdcolin/awesome-genome-visualization
Answer: RSeQC : infer_experiment.py Error: Could not retrieve index file
by
Trivas
★ 1.8k
You need to have indexed your bam/sam file using `samtools index`
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by
jared.andrews07
★ 16k
The simple answer is to plot it natively with plotly rather than use `ggplotly`. See [this stackoverflow answer](https://stackoverflow.com/…
Comment: Why does assigning genes with biomart give me different values than using a tran
by
GenoMax
142k
According to HUGO there is only one [**ZSCAN2 gene**][1] and it points to the first Ensembl gene ID (ENSG00000176371). Ensembl is annotatin…
Answer: RNAseq RNA content
by
noodle
▴ 580
There are many tools for this. I recommend [gatk (picard) CollectRnaSeqMetrics][1] or alternatively [RSeQC][2] and then run [multiqc][3…
Comment: Where to get the following bed file?
by
wyuan37
• 0
Hi, I emailed them and did get the bed file! Thank you so much.
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