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Showing :
questions
1
vote
0
replies
1.2k
views
different transcripts show hits to same gene but in different species, what is it showing?
blast
alignment
gene
updated 5.1 years ago by
Biostar
20 • written 8.3 years ago by
Farbod
★ 3.4k
6
votes
13
replies
14k
views
Showing FDR and log2FC in Volcano plot using R
R
RNA-Seq
volcano plot
updated 5.4 years ago by
zx8754
12k • written 6.9 years ago by
Farbod
★ 3.4k
17
votes
27
replies
5.6k
views
How to show both edgeR and deseq2 results in a single volcano plot; highliting overlaps
RNA-Seq
R
DEG
volcano plot
updated 5.4 years ago by
zx8754
12k • written 6.5 years ago by
Farbod
★ 3.4k
8
votes
6
replies
9.9k
views
How to just add some selected gene names to a volcano plot
R
ggplot2
volcano plot
updated 5.4 years ago by
zx8754
12k • written 6.5 years ago by
Farbod
★ 3.4k
5
votes
7
replies
2.0k
views
step by step BlastX against nr using Amazon cloud
blast
cloud
annotation
updated 5.6 years ago by
Abhishek
▴ 20 • written 7.0 years ago by
Farbod
★ 3.4k
0
votes
1
reply
3.5k
views
How to import a list of gene and visualize gene-gene interaction in Cytoscape zebrafish session
gene
Cytoscape
network
updated 5.8 years ago by
xanderpico
▴ 580 • written 7.9 years ago by
Farbod
★ 3.4k
2
votes
8
replies
4.4k
views
What is the prefered script for HISAT2 genome-guided using draft genome? --dta or --exon ?
RNA-Seq
alignment
HISAT2
genome guided
6.3 years ago by
Farbod
★ 3.4k
2
votes
2
replies
2.8k
views
Adding tag XS to HISAT2 sam files perior to StringTie
RNA-Seq
alignment
hisat2
stringtie
samtools
updated 6.4 years ago by
lakhujanivijay
5.9k • written 6.4 years ago by
Farbod
★ 3.4k
7
votes
7
replies
4.6k
views
Mapping paired-end reads to a draft genome using HISAT2
RNA-Seq
alignment
HISAT2
genome guided
updated 6.4 years ago by
GenoMax
147k • written 6.4 years ago by
Farbod
★ 3.4k
8
votes
4
replies
2.0k
views
What is the recent preference for RNA-seq read deposition perior to publication
SRA
RNA-Seq
repository
FAIRsharing
updated 6.4 years ago by
i.sudbery
20k • written 6.4 years ago by
Farbod
★ 3.4k
4
votes
5
replies
3.3k
views
running BUSCO on all isoforms or longest isoform per gene?
assembly
RNA-Seq
updated 6.5 years ago by
gilbert.bionet
▴ 160 • written 6.5 years ago by
Farbod
★ 3.4k
1
vote
1
reply
2.6k
views
How to perform univariate generalized linear models on RNA-seq data?
RNA-Seq
DEG
GLM
SARTools
updated 6.5 years ago by
h.mon
35k • written 6.5 years ago by
Farbod
★ 3.4k
0
votes
4
replies
2.1k
views
SARTools instalation error: DESeq2 1.10.1 was found but >= 1.12.0 is required
RNA-Seq
edgeR
DESeq2
SARTools
6.5 years ago by
Farbod
★ 3.4k
4
votes
9
replies
2.0k
views
How many of the SSR contained transcripts have ORF?
ORF
MISA
SSR
RNA-Seq
updated 6.9 years ago by
h.mon
35k • written 6.9 years ago by
Farbod
★ 3.4k
7
votes
7
replies
4.8k
views
Cytoscape network of upregulate and downregulate transcription factors: how to draw?
transcription factors
cytoscape
network
RNA-Seq
updated 6.9 years ago by
Leite
★ 1.3k • written 6.9 years ago by
Farbod
★ 3.4k
5
votes
12
replies
6.4k
views
How to download REVIGO TreeMap as Image? Also need help for Python script
python
revigo
GO
software error
updated 7.0 years ago by
Diwan
▴ 650 • written 7.0 years ago by
Farbod
★ 3.4k
8
votes
11
replies
3.9k
views
Semantic Similarity selection in REVIGO: which is better? many clusters or few?
go
revigo
gene ontology
7.0 years ago by
Farbod
★ 3.4k
4
votes
8
replies
2.7k
views
How to add GO pValue in blast2GO ?
go
annotation
REVIGO
Blast2GO
updated 7.0 years ago by
Puli Chandramouli Reddy
▴ 190 • written 7.0 years ago by
Farbod
★ 3.4k
9
votes
8
replies
2.1k
views
Why "Motile sperm domain-containing protein 2" has nothing to do with "sperm"?
gene
annotation
biology
updated 7.0 years ago by
harold.smith.tarheel
★ 5.0k • written 7.0 years ago by
Farbod
★ 3.4k
10
votes
23
replies
2.8k
views
Two simillarly annotated sequence has no alignment similarity. Why?
blast
alignment
gene
updated 7.0 years ago by
GenoMax
147k • written 7.0 years ago by
Farbod
★ 3.4k
0
votes
1
reply
1.3k
views
Is there any tools for Ortholog hit ratio calculation ?
blast
alignment
OHR
updated 7.6 years ago by
Biostar
20 • written 7.9 years ago by
Farbod
★ 3.4k
8
votes
13
replies
2.8k
views
Fold Change accepts, FDR denies; which one to use ?
RNA-Seq
FDR
DEG
FC
updated 7.7 years ago by
Devon Ryan
104k • written 7.7 years ago by
Farbod
★ 3.4k
0
votes
0
replies
1.5k
views
zero TMM : assembly error or biologically important phenomenon?
RNA-Seq
gene
7.8 years ago by
Farbod
★ 3.4k
4
votes
8
replies
2.1k
views
How to discover condition-dependent SNPs in transcriptomic data where each genes has several isofofrms ?
RNA-Seq
next-gen
Assembly
snp
SNP
7.8 years ago by
Farbod
★ 3.4k
4
votes
7
replies
1.5k
views
How to extract "High mobility group" sequence in multiple species ?
sequence
gene
alignment
High mobility group (HMG)
7.9 years ago by
Farbod
★ 3.4k
0
votes
6
replies
1.2k
views
Trapping sex specific SNPs from de novo transcriptome assembly: is it practical ?
SNP
RNA-Seq
Assembly
snp
7.9 years ago by
Farbod
★ 3.4k
3
votes
3
replies
2.9k
views
Tools for drawing and comparing linear diagram of amino acid sequences
gene
sequence
software
7.9 years ago by
Farbod
★ 3.4k
1
vote
0
replies
4.8k
views
showing row names and dendrogram in same side, using heatmap() or pheatmap()
R
software error
7.9 years ago by
Farbod
★ 3.4k
7
votes
11
replies
3.9k
views
Heatmap: how to just show significantly differentially expressed transcripts in it ?
R
RNA-Seq
heatmap
transcription factors
updated 7.9 years ago by
TriS
★ 4.7k • written 7.9 years ago by
Farbod
★ 3.4k
0
votes
0
replies
2.2k
views
How to Construct TF-based regulation network using Cytoscape software
Cytoscape
Transcription Factor
network
7.9 years ago by
Farbod
★ 3.4k
1
vote
5
replies
3.0k
views
How to report differentially expressed transcription factors in scatter plot
transcription factor
RNA-Seq
7.9 years ago by
Farbod
★ 3.4k
6
votes
8
replies
3.2k
views
Transcription factor discovery from RNA-seq data; Is it practical ?
blast
RNA-Seq
transcription factor
updated 7.9 years ago by
Devon Ryan
104k • written 7.9 years ago by
Farbod
★ 3.4k
0
votes
1
reply
1.2k
views
How to show the number of hits and the total number of each data-set protein in one graph?
blast
bar chart
7.9 years ago by
Farbod
★ 3.4k
0
votes
13
replies
3.0k
views
How to convert XP_002531646.1 to sp|P05661|MYSA_DROME in Diamond blastX output
blast
8.0 years ago by
Farbod
★ 3.4k
4
votes
7
replies
1.7k
views
collecting 50 most frequent proteins from tabular blastX result
blast
8.0 years ago by
Farbod
★ 3.4k
10
votes
15
replies
6.5k
views
DIAMOND blast imported into MEGAN6 has no taxonomic assignment
blast
MEGAN6
Taxonomy
DIAMOND
8.0 years ago by
Farbod
★ 3.4k
0
votes
1
reply
2.0k
views
Ortholog comparison between diploid and tetraploid species
software-error
ortholog
gene
sequence
updated 19 months ago by
Ram
44k • written 8.0 years ago by
Farbod
★ 3.4k
4
votes
15
replies
6.5k
views
comparing two lists using command line tools
sequence
blast
BASH
8.0 years ago by
Farbod
★ 3.4k
0
votes
3
replies
1.8k
views
How to use multifasta file in EMBOSS plotORF ?
software error
sequence
EMBOSS
ORF
updated 8.0 years ago by
Sej Modha
5.3k • written 8.0 years ago by
Farbod
★ 3.4k
6
votes
25
replies
2.8k
views
Why Markov model is depended to size of dataset?
software error
gene
sequence
HMM
8.0 years ago by
Farbod
★ 3.4k
2
votes
4
replies
1.9k
views
script for collecting selected IDs prediction result from Transdecoder .pep file
sequence
awk
bash script
python
8.0 years ago by
Farbod
★ 3.4k
4
votes
8
replies
2.5k
views
Does having ORF shows the coding potential of a transcript that showed no hit against NCBI nr ?
blast
gene
ORF
CDS
alignment
8.0 years ago by
Farbod
★ 3.4k
0
votes
3
replies
3.3k
views
how to parse XML blast output
blast
biopython
NCBIXML
8.0 years ago by
Farbod
★ 3.4k
8
votes
9
replies
5.2k
views
Find orthologs using EggNOG and local HMMER search for multiple transcripts
RNA-Seq
EggNOG
HMMER
orthologs
gene
updated 8.1 years ago by
jhc
★ 3.0k • written 8.1 years ago by
Farbod
★ 3.4k
16
votes
21
replies
2.6k
views
Why there are different hit for a same gene in different species
gene
blast
ortholog
paralog
8.1 years ago by
Farbod
★ 3.4k
6
votes
12
replies
6.4k
views
How to cite Ensembl
Ensembl
protein
cite
blast
updated 8.1 years ago by
crisime
▴ 290 • written 8.1 years ago by
Farbod
★ 3.4k
11
votes
10
replies
1.8k
views
Most fishes lay eggs, some are live-bearing, How to find related genes to these different charachteristics?
gene
reproduction
evolution
alignment
updated 8.1 years ago by
Biostar
20 • written 8.1 years ago by
Farbod
★ 3.4k
4
votes
5
replies
2.3k
views
Very simple ggplot2 histogram question
R
histogram
ggplot2
updated 8.1 years ago by
WouterDeCoster
47k • written 8.1 years ago by
Farbod
★ 3.4k
24
votes
20
replies
4.0k
views
how to draw COG Histogram ?
cog
clusters of orthologous groups
histogram
blast
updated 8.2 years ago by
GenoMax
147k • written 8.2 years ago by
Farbod
★ 3.4k
7
votes
8
replies
2.5k
views
how to include taxonomy information in blstx xml output ?
blast
BLASTGrabber
taxonomy in blast
xml
updated 8.2 years ago by
piet
★ 1.9k • written 8.2 years ago by
Farbod
★ 3.4k
63 results • Page
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