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184 results • Page
2 of 4
Sort: replies
Rank
Views
Votes
Replies
0
votes
4
replies
298
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
1 day ago by
DINESHR
• 0
0
votes
4
replies
228
views
Making multiple box plots with relative abundance in R
R
Boxplots
2 days ago by
ohtang7
▴ 40
1
vote
4
replies
133
views
Problematic fastq files...How can we trust them?
fastq
updated 1 hour ago by
Istvan Albert
99k • written 5 hours ago by
blackadder
▴ 30
0
votes
3
replies
4.0k
views
pheatmap lengends are being cutoff
pheatmap
legends
rstudio
heatmaps
updated 3 days ago by
Chris S.
▴ 320 • written 2.7 years ago by
enh
• 0
0
votes
3
replies
197
views
ERROR FILE EXTENSION
Prokka
1 day ago by
syirah4
• 0
5
votes
3
replies
267
views
SPAdes error: finished abnormally, OS return value: 21
SPAdes
updated 2 days ago by
Brian Bushnell
19k • written 3 days ago by
jiyoung
▴ 20
0
votes
3
replies
234
views
merged rs number information
merged
dbsnp
3 days ago by
sskimvd
• 0
2
votes
3
replies
1.0k
views
How to identify the 300 kb upstream and downstream genes of lncRNAs?
RNA-Seq
lncRNA
target genes
upstream
downstream
updated 6 days ago by
SeguraChain
• 0 • written 3.0 years ago by
mathavanbioinfo
▴ 70
0
votes
3
replies
303
views
Annovar - Annotated file cells show string
annovar
6 days ago by
Roshan
• 0
0
votes
3
replies
300
views
R ComplexHeatmap - Dividing Column Annotation into Distinct Y-Axis Scales
R
complexheatmap
updated 2 days ago by
jv
★ 1.2k • written 8 days ago by
TC_Chang
▴ 10
2
votes
3
replies
200
views
Blastn DB issue
cgmlst
blastn
updated 1 day ago by
Philipp Bayer
8.1k • written 2 days ago by
hakhasan
• 0
0
votes
3
replies
125
views
An incomprehensible error with R package gggenes
R
gggenes
visualize
updated 4 hours ago by
ATpoint
78k • written 6 hours ago by
alice005201314
• 0
6
votes
3
replies
273
views
BBDuk error: with these 4 lines....
BBDUK
trimming
java
4 days ago by
blackadder
▴ 30
0
votes
3
replies
374
views
Extracting list of identical items from several excel files
from
excel
items
Extract
file
updated 5 days ago by
DonPhager
• 0 • written 5 days ago by
otieno43
▴ 20
0
votes
3
replies
1.0k
views
Error with Ice normalization when running HiC-Pro
Hi-C
HiChIP
HiC-Pro
updated 4 days ago by
Cibo
• 0 • written 2.1 years ago by
Amina
• 0
0
votes
3
replies
195
views
In what case there are RR reads but no LL reads when detect inversions using IGV?
IGV
inversion
updated 22 hours ago by
Istvan Albert
99k • written 1 day ago by
Jingfang
• 0
6
votes
3
replies
219
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 1 day ago by
Jeremy
▴ 850 • written 2 days ago by
ohtang7
▴ 40
0
votes
3
replies
265
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
1 day ago by
cook.675
▴ 210
0
votes
3
replies
322
views
subset a bam file
bam
pysam
NGS
samtools
updated 5 days ago by
GenoMax
136k • written 6 days ago by
Ming
• 0
0
votes
3
replies
345
views
Alternatives to Music2 for rnaseq deconvolution without disease scRNA dataset
scRNA
deconvolution
Music
Music2
bulk
updated 6 days ago by
ATpoint
78k • written 6 days ago by
manuelmourato25
• 0
2
votes
3
replies
188
views
Is bisulfite-seq data from different studies comparable with each other?
Methylation
updated 1 day ago by
Basti
★ 1.9k • written 1 day ago by
CTLong
▴ 20
2
votes
3
replies
298
views
DEseq2 input
DEseq2
updated 3 days ago by
ATpoint
78k • written 4 days ago by
r.shiasi3897
▴ 10
1
vote
3
replies
264
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 2 days ago by
Nitin Narwade
★ 1.5k • written 3 days ago by
Bine
▴ 50
0
votes
3
replies
176
views
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics
nucleotide_diversity
vcf
1 day ago by
J
• 0
0
votes
2
replies
26
views
How Can I move the scattered dots more closer into the center of box ?
R
Boxplots
geom_jitter
updated 25 minutes ago by
Trivas
★ 1.5k • written 57 minutes ago by
ohtang7
▴ 40
0
votes
2
replies
273
views
Use of IDR after running MACS3 for ATAC-seq data
ATAC-seq
MACS2
MACS3
5 days ago by
Orange
▴ 10
1
vote
2
replies
263
views
Indexing by bowtie2 but aligning with STAR
STAR
mm10
Bowtie2
Alignment
Index
5 days ago by
Anojan
• 0
1
vote
2
replies
183
views
RnBeads which p-value to use
Methylation
RnBeads
updated 4 days ago by
ATpoint
78k • written 4 days ago by
a.basitkhan1990
▴ 30
0
votes
2
replies
689
views
CPAT: error on coding probability cutoff
lncRNA
RNAseq
CPAT
updated 4 days ago by
catarinaventura_pt
• 0 • written 21 months ago by
xiaoxia8923
• 0
0
votes
2
replies
202
views
RnBeads mean difference vs M-values
Methylation
updated 4 days ago by
Basti
★ 1.9k • written 4 days ago by
a.basitkhan1990
▴ 30
4
votes
2
replies
1.9k
views
Masurca. Failed to pre-correct Nanopore data, please check your data!
Nanopore
Masurca
updated 4 days ago by
colindaven
5.7k • written 2.4 years ago by
kamanovae
▴ 100
2
votes
2
replies
587
views
6 follow
Why runing scDblFinder before and after removing low QC cells gives different results
singleCellExperiment
scDblFinder
SMART-Seq
updated 3 days ago by
e.r.zakiev
▴ 170 • written 5 months ago by
Assa Yeroslaviz
★ 1.8k
3
votes
2
replies
192
views
Running STAR on fastq file generated from a RNA-seq experiment
STAR
RNAseq
fastq
files
updated 3 days ago by
Darked89
4.5k • written 3 days ago by
achanda
• 0
0
votes
2
replies
213
views
how to use pilon
genome
pipelines
assembly
pilon
contig
updated 3 days ago by
Arup Ghosh
3.2k • written 9 days ago by
vasudhapai
• 0
0
votes
2
replies
222
views
using RSEM with non Trinity assembly
SPAdes
Trinity
RSEM
3 days ago by
jen
• 0
0
votes
2
replies
287
views
Find Genes in Homer Analysis that have the enriched Motif
single
ORA
nucleus
mRNA
Homer
3 days ago by
je71xusa
• 0
1
vote
2
replies
242
views
Best practices for unstranded sequences in featureCounts
featurecounts
overlapping
unstranded
3 days ago by
Enrique
• 0
3
votes
2
replies
639
views
CPTAC data, download, merge
CPTAC
merging
seq
data
RNA
updated 3 days ago by
Mohita
▴ 50 • written 16 months ago by
Rob
▴ 160
1
vote
2
replies
226
views
Comparing 3 Data Sets using DeSeq and Heatmaps
DeSeq
Normalization
2 days ago by
harter-ainsworth.izaak
• 0
3
votes
2
replies
198
views
Moving AF tag to new column in a VCF file
mutect2
vcf
2 days ago by
Christian
▴ 30
2
votes
2
replies
640
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 2 days ago by
cmdcolin
★ 3.4k • written 2 days ago by
Dylan C-C
• 0
0
votes
2
replies
316
views
Help doing differential expression analysis -experimental design and gProfiler TF interpretation-
gProfiler
mRNA
Differential-expression
TCGA
updated 2 days ago by
rajabolacuan
• 0 • written 9 days ago by
Camilo Andres
▴ 40
0
votes
2
replies
1.4k
views
AttributeError: module 'collections' has no attribute 'Hashable'
Spades
updated 2 days ago by
jiyoung
▴ 20 • written 7 months ago by
Hayler Edu
▴ 30
1
vote
2
replies
197
views
Problem in installing 'magick' R package
R
installation
package
magick
updated 2 days ago by
DBScan
▴ 210 • written 2 days ago by
applepie
• 0
3
votes
2
replies
958
views
How do I download a list of genes involved in cellular metabolism (in humans) based on a Reactome pathway?
genes
metabolism
GO
Reactome
updated 1 day ago by
el24
▴ 40 • written 2.0 years ago by
emmah
• 0
1
vote
2
replies
202
views
What type of cancer did they study in this paper?
cancer
RNAseq
single-cell
updated 1 day ago by
GenoMax
136k • written 1 day ago by
JACKY
▴ 120
1
vote
2
replies
192
views
How can I amend the output of a DIAMOND python script?
Python
Diamond
COG_analysis
1 day ago by
eamaunders
• 0
3
votes
2
replies
262
views
Mapping quality in `vg giraffe`
vg
1 day ago by
Wenhai
• 0
0
votes
2
replies
221
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 1 day ago by
fracarb8
★ 1.3k • written 1 day ago by
synat.keam
▴ 80
2
votes
2
replies
192
views
R script in docker
R
Visual_studio_code
Docker
1 day ago by
mrashad
▴ 70
184 results • Page
2 of 4
Recent Votes
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
Answer: 1000 genomes project reference panel - GRCh38
Answer: 1000 genomes project reference panel - GRCh38
Comment: IMPUTE2- Map file for custom reference panel
IMPUTE2- Map file for custom reference panel
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Answer: How Can I move the scattered dots more closer into the center of box ?
by
Trivas
★ 1.5k
You added a position dodge on your boxplot but not on your points.
Comment: How Can I move the scattered dots more closer into the center of box ?
by
ATpoint
78k
Please understand that biostars is not a helpdesk for trivial ggplot questions. Google it and find help on previous StackExchange sites, or…
Comment: Yes .. BBMap can do that! - Part III clumpify (mark (and dedupe) duplicates with
by
jucosie
• 0
Hello, I am reviewing some old scripts in which I used clumpify.sh (BBMap 38.90) with the following parameters: ./clumpify.sh in1=$dir_c…
Comment: Problematic fastq files...How can we trust them?
by
Istvan Albert
99k
perhaps ask her about the origin of the data, how was the data postprocessed FASTQ data is a bit more resilient than other types of data a…
Answer: GO categorization
by
Istvan Albert
99k
If you have an organism that lacks the GO to gene mapping then you have to find a way to assign these terms to your genes. Basically your …
Comment: doubt about usage of megahit
by
Istvan Albert
99k
you have not mentioned what kind of resources you have, how much data you have to process and what the expected genome/transcriptome sizes …
Comment: Problematic fastq files...How can we trust them?
by
ATpoint
78k
Then tell her to bring proper data. In the lab you also don't use buffers with mold growing in it, and in bioinformatics we don't start wit…
Comment: Problematic fastq files...How can we trust them?
by
blackadder
▴ 30
Its not my data. An external researcher is visiting and she wanted from us to do some bioinformatics... The samples were not sequenced by u…
Comment: Tools or R / Python packages to perfom ML models
by
sil_bioinfo
▴ 30
Oh, I understand. Thank you so much for your help! The truth is that there is so much information, so many packages, libraries, tutorials,…
Comment: Tools or R / Python packages to perfom ML models
by
Matthias Zepper
4.2k
Just to clarify: Many ML models are trained and executed using dedicated software libraries for machine learning and artificial intellige…
Answer: Problematic fastq files...How can we trust them?
by
ATpoint
78k
> I assume that maybe all these are fixable with a script but my question is, can we trust these files? Is it worth spending time and effor…
Comment: Tools or R / Python packages to perfom ML models
by
sil_bioinfo
▴ 30
My main idea is to be able to classify patients with active TB, LTBI and healthy patients as well as possible. The problem is that within t…
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
by
rpolicastro
12k
They could have saved themselves a ton of money by sequencing this on a miseq.
Comment: Annotate Unplaced Scaffold with Chromosome Information
by
cmdcolin
★ 3.4k
I think there are tools like ragtag https://github.com/malonge/RagTag that could help. you can also align your reads back to your new assem…
Comment: An incomprehensible error with R package gggenes
by
ATpoint
78k
It's not stupid, just a bit lazy ;-)
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