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408 results • Page
1 of 9
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Views
Votes
Replies
287
votes
39
replies
182k
views
29 follow
Tutorial:
How to download raw sequence data from GEO/SRA
fastq
SRA
bam
GEO
updated 12 months ago by
Ram
43k • written 9.6 years ago by
Obi Griffith
20k
296
votes
33
replies
107k
views
25 follow
Tutorial:
Cheat Sheet For One-Based Vs Zero-Based Coordinate Systems
coordinates
updated 13 months ago by
Ram
43k • written 10.4 years ago by
Obi Griffith
20k
239
votes
176
replies
94k
views
73 follow
Tutorial:
Survival analysis of TCGA patients integrating gene expression (RNASeq) data
RNA-Seq
Survival
TCGA
updated 10 months ago by
Ram
43k • written 8.7 years ago by
TriS
★ 4.7k
93
votes
23
replies
90k
views
15 follow
Tutorial:
How to Install SamTools, HTSLib, and BCFTools on Ubuntu 18.04
bcftools
samtools
htslib
updated 9 weeks ago by
clara.apicella
• 0 • written 5.7 years ago by
otwtgin2010
▴ 610
54
votes
14
replies
89k
views
10 follow
Tutorial:
Using R in Conda
R
updated 12 months ago by
Ram
43k • written 3.7 years ago by
rohitsatyam102
▴ 840
139
votes
25
replies
83k
views
14 follow
Tutorial:
Piping With Samtools, Bwa And Bedtools
unix
samtools
bwa
bedtools
updated 24 months ago by
Ram
43k • written 11.9 years ago by
Ying W
★ 4.2k
29
votes
10
replies
80k
views
9 follow
Tutorial:
Installing an updated R version (>=4.0) using conda
software-error
R
updated 12 months ago by
Ram
43k • written 3.0 years ago by
Nitin Narwade
★ 1.6k
196
votes
44
replies
71k
views
33 follow
Tutorial:
Analysing Microarray Data In Bioconductor
microarray-analysis
bioconductor
updated 14 months ago by
Ram
43k • written 11.5 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 17 months ago by
Ram
43k • written 10.4 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 13 months ago by
Ram
43k • written 11.3 years ago by
vijay
★ 1.6k
87
votes
2
replies
58k
views
6 follow
Tutorial:
How To Ask Good Questions On Technical And Scientific Forums
how-to
updated 13 months ago by
Ram
43k • written 10.8 years ago by
Eric Normandeau
11k
2
votes
1
reply
58k
views
Tutorial:
Docker denied: requested access to the resource is denied
docker
updated 20 months ago by
LauferVA
4.1k • written 20 months ago by
kodwings
▴ 20
147
votes
34
replies
54k
views
17 follow
Tutorial:
Working with MAF files (Mutation Annotation Format) from the TCGA (The Cancer Genome Atlas)
music
cancer
tcga
mutation
maf
updated 13 months ago by
Ram
43k • written 11.0 years ago by
Cyriac Kandoth
6.0k
0
votes
3
replies
52k
views
Tutorial:
Installation VMD on LINUX_64
gromacs
VMD
updated 11 months ago by
Ram
43k • written 7.8 years ago by
Hassan Rasouli
▴ 10
149
votes
70
replies
50k
views
20 follow
Tutorial:
Network plot from expression data in R using igraph
microarray
RNA-Seq
R
network
updated 7 months ago by
Raheleh
▴ 260 • written 6.4 years ago by
Kevin Blighe
87k
66
votes
9
replies
49k
views
7 follow
Tutorial:
Reference Assembly - Mapping Reads To A Reference Genome
reference
samtools
mapping
bwa
updated 13 months ago by
Ram
43k • written 10.8 years ago by
Joseph Hughes
★ 3.0k
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 12 months ago by
Ram
43k • written 5.7 years ago by
ATpoint
81k
97
votes
105
replies
45k
views
25 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III - Version 2
1000genomes
PLINK
PCA
updated 12 months ago by
Ram
43k • written 5.6 years ago by
Kevin Blighe
87k
53
votes
19
replies
43k
views
6 follow
Tutorial:
Visualizing Chip-Seq Data Using Ucsc [Bigwig]
visualization
bigwig
chip-seq
rna-seq
updated 13 months ago by
Ram
43k • written 12.0 years ago by
Sukhi Singh
11k
60
votes
52
replies
43k
views
23 follow
Tutorial:
Creating Interactive Volcano Plots with R and Plot.ly
plotly
R
volcano-plot
updated 12 months ago by
Ram
43k • written 7.5 years ago by
steve
★ 3.5k
58
votes
25
replies
40k
views
15 follow
Tutorial:
Protocol To Downlad TCGA Data From GDC
GDC
methylation
TCGA
updated 12 months ago by
Ram
43k • written 7.7 years ago by
Shicheng Guo
★ 9.4k
74
votes
3
replies
39k
views
Tutorial:
Revisiting the FastQC read duplication report
fastqc
updated 2.4 years ago by
Ram
43k • written 9.7 years ago by
Istvan Albert
100k
133
votes
123
replies
37k
views
23 follow
Tutorial:
Survival analysis with gene expression
cox
gene-expression
survival-analysis
geo
updated 12 months ago by
1769mkc
★ 1.2k • written 5.4 years ago by
Kevin Blighe
87k
45
votes
2
replies
37k
views
Tutorial:
Mapping Reads With Bwa And Bowtie
bowtie
bwa
updated 13 months ago by
Ram
43k • written 12.0 years ago by
MSU course 2011
▴ 540
39
votes
16
replies
36k
views
16 follow
Tutorial:
installing samtools with conda - overcoming two common errors
samtools
conda
updated 3 months ago by
GenoMax
140k • written 3.6 years ago by
lavinia.gordon
▴ 160
99
votes
16
replies
33k
views
18 follow
Tutorial:
Heatmaps in R
heatmap
R
updated 12 months ago by
Ram
43k • written 7.6 years ago by
Jean-Karim Heriche
27k
90
votes
48
replies
33k
views
29 follow
Tutorial:
Extract Total Non-Overlapping Exon Length Per Gene With Bioconductor
fpkm
rna-seq
bioconductor
updated 4 months ago by
Ram
43k • written 10.4 years ago by
Irsan
★ 7.8k
95
votes
25
replies
33k
views
11 follow
Tutorial:
Fastq Quality Control Shootout
quality
qc
trimming
fastq
updated 13 months ago by
Ram
43k • written 11.5 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 13 months ago by
Ram
43k • written 10.4 years ago by
Obi Griffith
20k
84
votes
29
replies
31k
views
20 follow
Tutorial:
How to create a mutation landscape (waterfall) plot with GenVisR
BioConductor
GenVisR
Graphics
R
updated 8 months ago by
amziepickles
• 0 • written 8.1 years ago by
Obi Griffith
20k
142
votes
21
replies
30k
views
12 follow
Tutorial:
A few words for R beginners
Swirl
R
updated 23 months ago by
Ram
43k • written 9.3 years ago by
Parham
★ 1.6k
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 13 months ago by
Ram
43k • written 10.4 years ago by
Istvan Albert
100k
99
votes
8
replies
29k
views
8 follow
Tutorial:
Guide to TCGA data
cancer
RNA-Seq
clinical
TCGA
updated 11 months ago by
Ram
43k • written 8.1 years ago by
Jordan Anaya
★ 1.1k
73
votes
27
replies
27k
views
16 follow
Tutorial:
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
RNA-seq
updated 3 months ago by
snardeli
• 0 • written 10.1 years ago by
Istvan Albert
100k
73
votes
60
replies
27k
views
16 follow
Tutorial:
Produce PCA bi-plot for 1000 Genomes Phase III in VCF format (old)
1000genomes
PLINK
PCA
VCF
updated 13 months ago by
Ram
43k • written 6.6 years ago by
Kevin Blighe
87k
67
votes
6
replies
26k
views
7 follow
Tutorial:
Rna-Seq Review Papers
RNA-seq
papers
updated 13 months ago by
Ram
43k • written 11.6 years ago by
Istvan Albert
100k
104
votes
6
replies
26k
views
6 follow
Tutorial:
Creating workflows with snakemake and conda
workflow
snakemake
conda
updated 12 months ago by
Ram
43k • written 5.6 years ago by
finswimmer
16k
44
votes
6
replies
24k
views
Tutorial:
Greatly speed up conda by using mamba
software
updated 2.2 years ago by
cameron.cowan
▴ 40 • written 3.0 years ago by
rpolicastro
13k
42
votes
16
replies
23k
views
15 follow
Tutorial:
Tutorial: Analyze exome Copy number variation (CNV) in single patient or in population.
GISTIC
varscan2
CNV
copy-number
updated 19 months ago by
Ram
43k • written 8.5 years ago by
Chirag Nepal
★ 2.4k
10
votes
5
replies
23k
views
Tutorial:
Y-DNA and mtDNA Haplogroup Predictor
haplogroup
updated 12 months ago by
Ram
43k • written 5.7 years ago by
Shicheng Guo
★ 9.4k
51
votes
3
replies
23k
views
Tutorial:
Sam File Format - Lesser Known Tips And Tricks
sam
updated 13 months ago by
Ram
43k • written 11.2 years ago by
Ya
▴ 300
85
votes
21
replies
22k
views
16 follow
Tutorial:
Gene Set Enrichment Analysis
microarray
enrichment
RNA-Seq
GSEA
updated 12 months ago by
Ram
43k • written 3.5 years ago by
Hamid Ghaedi
3.2k
30
votes
6
replies
22k
views
Tutorial:
Transforming And Manipulating Color Space Reads
conversion
solid
updated 18 months ago by
Ram
43k • written 11.9 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 12 months ago by
Ram
43k • written 6.5 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 9 days ago by
aUser
▴ 30 • written 7.5 years ago by
martinguerrerog89
▴ 310
39
votes
6
replies
19k
views
Tutorial:
Creating chromosome karyotype plot with R and ggplot2
ggplot2
R
chromosome
karyotype
updated 10 months ago by
Ram
43k • written 6.6 years ago by
steve
★ 3.5k
14
votes
3
replies
19k
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 7 months ago by
William
▴ 30 • written 7.0 years ago by
kirannbishwa01
★ 1.6k
76
votes
70
replies
19k
views
18 follow
Tutorial:
Clustering of DAVID gene enrichment results from gene expression studies
enrichment
david
updated 12 months ago by
Ram
43k • written 6.1 years ago by
Kevin Blighe
87k
83
votes
34
replies
18k
views
22 follow
Tutorial:
Enrichment Analysis, Clustering and Scoring with pathfindR
enrichment
R
pathway
active-subnetwork
updated 10 months ago by
adelheidkratzer
• 0 • written 5.8 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 3.7 years ago by
krishdb38
• 0 • written 7.8 years ago by
Esaie
▴ 170
408 results • Page
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Comment: Centromere and telomere positions for Chm13v2 assembly
C: Last column in UCSC cytoBands.txt files
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
F*up Night style events for Bioinformatics ? Comment if you're interested!
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
Comment: Gene reads all zero for each sample
Comment: Gene reads all zero for each sample
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Comment: Parsing fasta file by coordinates
by
GenoMax
140k
> A lot of the responses are addressing problems other than the one I have You could have said clearly that you are referring to co-ordin…
Comment: Low number of both surviving reads after trimming
by
Ram
43k
Please edit your post and add the code parts again, this time use the `101010` code button and NOT the double quote button. The latter is u…
Answer: F*up Night style events for Bioinformatics ? Comment if you're interested!
by
Pierre Lindenbaum
160k
... reminds me [https://twitter.com/yokofakun/status/1267877851795259397][1] ( my twitter account is now private) ![ops][2] [1]: https…
Comment: Flow Cytometry Data Analysis by Seurat
by
Ram
43k
Why did you delete this post, https://www.biostars.org/u/142036/ ?
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
by
dariober
14k
Perhaps more concerning is why you have features (genes?) with small pvalue but fold-change very close to zero. It's also unusual that ther…
Comment: Gene reads all zero for each sample
by
DYLAN NICO
• 0
Thank you for the suggestions. Unfortunately I cannot add any details for lack of information. But I will try using a different alignment a…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
They are +ve and -ve strands, but identical two by two ... I can filter that out later on. This is probably a very naive question, but what…
Comment: Gene reads all zero for each sample
by
ATpoint
81k
Do I understand correctly that you have one gene you are interested in, but all counts are zero, right? If so, first thing could be to use …
Answer: ONT direct RNA sequencing
by
joe
▴ 470
You should use `cat` on .gz files, part of the magic of .gz ...I guess if you use `zcat` they are unzipped and this is why you get the erro…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you !!
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by
Zhenyu Zhang
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You can only have one active token at a time, but you can copy the same token as many times as you want and use them in different computers…
Comment: Parsing fasta file by coordinates
by
sorrymouse
▴ 120
Yes, thats correct. A lot of the responses are addressing problems other than the one I have - I don't want to cluster the sequences based …
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Not sure if I am missing something but you want 4 copies of the same sequence with a different fasta header?
Comment: Normalization strategies for comparing mapped reads across samples in RNA-seq
by
Ram
43k
> TPM seems like a good method, but it may not be suitable here because it requires gene/transcript length. Also because TPM cannot be com…
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I did run the `JoinLayers()` even then it is not working, here is the output before and after ```r DefaultAssay(combined1) <- 'RNA' com…
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