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27 results • Page
1 of 1
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0
votes
0
replies
5
views
deeptools k-means clustering
heatmap
deeptools
chipseq
5 minutes ago by
biology_inform
▴ 50
0
votes
0
replies
10
views
filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts
align
bbmap
metagenomics
22 minutes ago by
Bryan
▴ 10
0
votes
0
replies
14
views
How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
plasmid
chipseq
1 hour ago by
tss243
• 0
1
vote
2
replies
79
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 4 hours ago by
ATpoint
78k • written 4 hours ago by
ohtang7
▴ 30
0
votes
0
replies
37
views
Conumee output as input for Gistic2.0
cnv
copy
gistic
cna
conumee
updated 4 hours ago by
GenoMax
136k • written 5 hours ago by
sativus
▴ 10
0
votes
0
replies
46
views
Population study based on metaT and MetaG
metagenome
metatranscriptome
study
population
updated 5 hours ago by
GenoMax
136k • written 5 hours ago by
PierreGT
• 0
0
votes
0
replies
48
views
sequencing deep mutational scanning library
mutagenesis
illumina
long-read
sequencing
6 hours ago by
reaset41
• 0
0
votes
0
replies
40
views
GMT file from eggnog annotation
gmt
annotation
Eggnog
6 hours ago by
jorge.cortes.miranda
• 0
0
votes
1
reply
103
views
How can I amend the output of a DIAMOND python script?
Python
Diamond
COG_analysis
updated 7 hours ago by
Nitin Narwade
★ 1.5k • written 9 hours ago by
eamaunders
• 0
1
vote
2
replies
147
views
Problem in installing 'magick' R package
R
installation
package
magick
updated 11 hours ago by
DBScan
▴ 210 • written 14 hours ago by
applepie
• 0
0
votes
2
replies
174
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
updated 10 hours ago by
GenoMax
136k • written 1 day ago by
cook.675
▴ 200
0
votes
1
reply
116
views
How to create a mutation frequency comparison plot?
R
data-visualization
plot
updated 7 hours ago by
rpolicastro
12k • written 15 hours ago by
saipra003
▴ 10
0
votes
0
replies
75
views
How to find node Postion and source(sample) ?
vg
16 hours ago by
zhang yi xing
▴ 20
0
votes
3
replies
195
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
updated 9 hours ago by
ATpoint
78k • written 21 hours ago by
DINESHR
• 0
0
votes
0
replies
69
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle
protein
alignment
17 hours ago by
Richard Fontaine
• 0
2
votes
5
replies
195
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
updated 1 hour ago by
tshtatland
▴ 170 • written 17 hours ago by
cee28
▴ 20
0
votes
2
replies
282
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 19 hours ago by
cmdcolin
★ 3.4k • written 20 hours ago by
Dylan C-C
• 0
3
votes
4
replies
243
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 10 hours ago by
Nitin Narwade
★ 1.5k • written 21 hours ago by
RNAseqer
▴ 250
1
vote
6
replies
296
views
Discrepancy in total number of bases in trimmed read1 and read2 files after BBDuk
bbduk
15 hours ago by
CTLong
▴ 10
0
votes
6
replies
309
views
Best practices for differential expression analysis with low-yield Nanopore/ONT direct cDNA data?
RNA-Seq
Nanopore
ONT
differential
expression
2 hours ago by
tw_140
• 0
9
votes
16
replies
685
views
Construction of single sequence assembly out of contigs
Contigs
Bacteria
Genome
WGS
21 hours ago by
analyst
▴ 10
0
votes
1
reply
145
views
Harmony integration PC variance explained
scRNA
integration
harmony
updated 8 hours ago by
CTLong
▴ 10 • written 2 days ago by
e.iich
• 0
0
votes
0
replies
125
views
Mapping Mouse RNAseq Marker Genes to Reactome Pathways
single-cell
pathways
reactome
RNAseq
gene
2 hours ago by
el24
▴ 40
1
vote
6
replies
496
views
frequency plot for peaks
chip-seq
chipseeker
updated 18 hours ago by
Ankit
▴ 400 • written 16 days ago by
Mehwish
▴ 10
1
vote
1
reply
169
views
Match variants for allele frequency, LD score, and other features
snp
3 hours ago by
Jautis
▴ 520
0
votes
2
replies
1.4k
views
AttributeError: module 'collections' has no attribute 'Hashable'
Spades
updated 13 hours ago by
jiyoung
▴ 20 • written 7 months ago by
Hayler Edu
▴ 30
0
votes
1
reply
329
views
How to use conumee segment mean for gistic input
genomics
gistic
NGS
methylation
conumee
updated 5 hours ago by
sativus
▴ 10 • written 14 months ago by
Thind amarinder
▴ 340
27 results • Page
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Recent Votes
How to make a survival plot for a gene between High expression and low expression samples?
Comment: bwa mem hangs after a few thousand reads
bwa mem hangs after a few thousand reads
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
How To Separate Illumina Based Strand Specific Rna-Seq Alignments By Strand
Answer: Generate Read counts from bam file
Comment: Generate Read counts from bam file
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Answer: Where is the index command?
by
Michael
53k
There is a ready-made package for samtools, simply do apt install samtools Also, your screenshot shows you are using the root account…
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 170
Use option `-v` with value of 4 or above to help diagnose the issue: `-v INT` Control the verbose level of the output. This option has not…
Comment: bwa mem hangs after a few thousand reads
by
tshtatland
▴ 170
Cross-posted here: [sequence alignment - bwa mem hangs after a few thousand reads - Bioinformatics Stack Exchange](https://bioinformatics.s…
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
• 0
Thank you, I really appreciate your insight! I will look into the dropouts I have.
Answer: Generate Read counts from bam file
by
NextGenSeek
• 0
Are you analysing RNA or DNA heteroplasmy levels?
Comment: What type of cancer did they study in this paper?
by
GenoMax
136k
Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …
Comment: p-value combination methods
by
i.sudbery
18k
edgeR *is* an NB-GLM. The input to NB-GLMs, including edgeR and DESeq is read counts from each sample.
Answer: What type of cancer did they study in this paper?
by
jared.andrews07
★ 16k
Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
Comment: p-value combination methods
by
sehriban.buyukkilic
• 0
its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
Comment: How do I download a list of genes involved in cellular metabolism (in humans) ba
by
el24
▴ 40
Hi @pratik, Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-spe…
Comment: Match variants for allele frequency, LD score, and other features
by
Jautis
▴ 520
Trying to bump this
Comment: p-value combination methods
by
i.sudbery
18k
The parameters you have here are the *output* of an NB-GLM, not the input to an NB-GLM (most likely edgeR?)
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
ATpoint
78k
Please provide data as dput(), not via any random dropbox, that could be anything (also malware, theoretically). If log transformation crea…
Comment: Extracting chimeric reads from mapping
by
doggie
• 0
Hi Pierre, so does samjdk support single-end reads for extracting chimeric reads? I've aligned my virus to the human reference, sorted the …
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
dthorbur
▴ 870
You can try `scale_y_sqrt()` instead if you don't like the look of the log10 transformation. As an aside, it doesn't look like your fill va…
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